ABAQUS
Engineering
Mahuika
Gpu
Mpi
Omp
Fea
Mahuika
Maui
Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
Available Modules
Licence
ABAQUS is proprietary software.
Access to a valid licence token is required to run ABAQUS.
Institution | Faculty | Uptime | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
University of Auckland | Faculty of Engineering | 98% | ||||||||||||
|
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University of Waikato | 99% |
ABRicate
Mahuika
Mass screening of contigs for antimicrobial and virulence genes
Available Modules
Links
ABySS
Biology
Mahuika
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
Available Modules
Links
ACTC
Mahuika
ACTC converts independent triangles into triangle strips or fans.
Available Modules
Links
AGAT
Mahuika
Suite of tools to handle gene annotations in any GTF/GFF format.
Available Modules
Links
AGE
Mahuika
Alignment of sequences with structural variants.
Available Modules
Links
AMOS
Mahuika
Collection of tools for genome assembly
Available Modules
Links
AMRFinderPlus
Mahuika
NCBI Antimicrobial Resistance Gene Finder Plus
Available Modules
Links
ANIcalculator
Mahuika
Calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes.
Available Modules
Links
ANNOVAR
Mahuika
Efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes .
Available Modules
Links
ANSYS
Engineering
Visualisation
Mahuika
Application
Mahuika
Maui
Maui_ancil
Available Modules
Licence
ANSYS is proprietary software.
Access to a valid licence token is required to run ANSYS.
Institution | Faculty | Uptime | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
University of Auckland | Faculty of Engineering | 72% | |||||||||
Orbis Diagnostics | 100% | ||||||||||
Auckland University of Technology | Faculty of Engineering | 72% | |||||||||
University of Waikato | 72% | ||||||||||
University of Canterbury | 99% | ||||||||||
University of Otago | 99% | ||||||||||
|
ANTS
Maui_ancil
Ants is a versatile, easy to use Python library for developing ancillary applications. This package is restricted to the UM user group.
Available Modules
Links
ANTs
Mahuika
ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
Available Modules
Links
AOCC
Mahuika
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
Available Modules
Links
AOCL-BLIS
Mahuika
Optimized version of BLIS for AMD EPYC family of processors..
Available Modules
Links
AOCL-FFTW
Mahuika
Optimized version of FFTW for AMD EPYC family of processors.
Available Modules
Links
AOCL-ScaLAPACK
Mahuika
Optimized version of ScaLAPACK for AMD EPYC family of processors.
Available Modules
Links
APR
Mahuika
Apache Portable Runtime (APR) libraries.
Available Modules
Links
APR-util
Mahuika
Apache Portable Runtime (APR) util libraries.
Available Modules
Links
ARIBA
Mahuika
Antimicrobial Resistance Identification By Assembly
Available Modules
Links
ASAGI
Mahuika
a pArallel Server for Adaptive GeoInformation
Available Modules
Links
ATK
Mahuika
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.
Available Modules
Links
AUGUSTUS
Biology
Mahuika
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
Available Modules
module load AUGUSTUS/3.5.0-gimkl-2022a
Links
Abseil
Mahuika
Collection of C++ library code designed to augment the C++ standard library.
Available Modules
Links
AdapterRemoval
Mahuika
Ssearches for and removes remnant adapter sequences from High-Throughput Sequencing data.
Available Modules
Links
AdaptiveCpp
Mahuika
AdaptiveCpp (formerly hipSYCL) is a SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP
Available Modules
Links
Advisor
Mahuika
Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
Available Modules
Links
AlphaFold
Mahuika
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
Available Modules
AlphaFold2DB
Mahuika
AlwaysIntelMKL
Mahuika
Overrides the MKL internal utility function mkl_serv_intel_cpu_true so that AVX2 optimised kernels will be used, even when running on an AMD CPU.
Available Modules
Links
Anaconda2
Machine_learning
Maui_ancil
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. IMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up certain types of mathematical computations, such as linear algebra or FFT. The module sets MKL_NUM_THREADS=1 to run MKL on a single thread by default, avoiding accidental oversubscription of cores. The number of threads can be increased for large problems, please refer to the Intel MKL documentation for guidance.
Available Modules
Links
Anaconda3
Machine_learning
Mahuika
Maui_ancil
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
Available Modules
module load Anaconda3/2021.05-gimkl-2020a
module load Anaconda3/2020.02-GCC-7.1.0
Links
Apptainer
Mahuika
Armadillo
Mahuika
C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.
Available Modules
Links
Arrow
Mahuika
Maui_ancil
Apache Arrow, a cross-language development platform for in-memory data.
Available Modules
module load Arrow/14.0.1-GCC-12.3.0
module load Arrow/8.0.0-GCCcore-9.2.0
Links
Aspera-CLI
Mahuika
IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.
Available Modules
Links
AutoDock-GPU
Mahuika
OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.
Available Modules
Links
AutoDock_Vina
Mahuika
AutoDock Vina is an open-source program for doing molecular docking.
Available Modules
Links
Autoconf-archive
Mahuika
A collection of more than 500 macros for GNU Autoconf
Available Modules
BBMap
Biology
Mahuika
BBMap short read aligner, and other bioinformatic tools.
Available Modules
module load BBMap/39.01-GCC-11.3.0
Links
BCFtools
Biology
Mahuika
Manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
Available Modules
module load BCFtools/1.19-GCC-11.3.0
Links
BCL-Convert
Mahuika
Converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files
Links
BEAST
Biology
Mahuika
Bayesian MCMC phylogenetic analysis of molecular sequences for reconstructing phylogenies and testing evolutionary hypotheses.
Available Modules
Links
BEDOPS
Biology
Mahuika
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
Available Modules
Links
BEDTools
Biology
Mahuika
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
Available Modules
module load BEDTools/2.30.0-GCC-11.3.0
Links
BEEF
Chemistry
Mahuika
Maui
BEEF is a library implementing the Bayesian Error Estimation Functional, a description of which can be found here: http://dx.doi.org/10.1103/PhysRevB.85.235149
Available Modules
module load BEEF/0.1.1-r16-intel-2022a
module load BEEF/0.1.1-r16-CrayIntel-23.02-19
Links
BGC-Bayesian-genomic-clines
Mahuika
Collection of code for Bayesian genomic cline analyses.
Available Modules
BLAST
Biology
Mahuika
Mahuika
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
Available Modules
module load BLAST/2.13.0-GCC-11.3.0
BLASTDB
Mahuika
BLAT
Biology
Mahuika
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Available Modules
Links
BLIS
Mahuika
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
Available Modules
Links
BOLT-LMM
Mahuika
The BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis
Available Modules
Links
BRAKER
Mahuika
Pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
Available Modules
module load BRAKER/3.0.3-gimkl-2022a-Perl-5.34.1
BUSCO
Biology
Mahuika
Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
Available Modules
module load BUSCO/5.6.1-gimkl-2022a
Links
BWA
Biology
Mahuika
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
Available Modules
module load BWA/0.7.17-gimkl-2017a
Links
BamTools
Biology
Mahuika
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
Available Modules
Links
Bandage
Mahuika
Bandage is a program for visualising de novo assembly graphs
Available Modules
Links
Basilisk
Mahuika
Maui_ancil
Basilisk is a Free Software program for the solution of partial differential equations on adaptive Cartesian meshes.
Available Modules
module load Basilisk/20220324-gimpi-2020a
module load Basilisk/20180226-gimpi-2018b
Links
BayPass
Mahuika
Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables
Available Modules
Links
BayeScan
Mahuika
Identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
Available Modules
Links
BayesAss
Mahuika
Program for inference of recent immigration rates between populations using unlinked multilocus genotypes
Available Modules
Links
Bazel
Mahuika
Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
Available Modules
module load Bazel/3.7.2-GCCcore-9.2.0
Links
Beagle
Mahuika
Package for phasing genotypes and for imputing ungenotyped markers.
Available Modules
Links
BiG-SCAPE
Mahuika
Constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).
Available Modules
Links
Bifrost
Mahuika
Highly parallel construction, indexing and querying of colored and compacted de Bruijn graphs.
Available Modules
Links
Bio-DB-BigFile
Mahuika
Read BigWig and BigBed genome feature databases
Available Modules
module load Bio-DB-BigFile/1.07-GCC-11.3.0-Perl-5.34.1
Links
Bio-DB-HTS
Mahuika
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
Available Modules
module load Bio-DB-HTS/3.01-GCC-11.3.0-Perl-5.34.1
Links
BioPP
Mahuika
Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.
Available Modules
Links
Bismark
Biology
Mahuika
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Available Modules
Links
BlenderPy
Mahuika
Blender provides a pipeline for 3D modeling, rigging, animation, simulation, rendering, compositing, motion tracking, video editing and 2D animation. This particular build of Blender provides a Python package 'bpy' rather than the stand-alone application.
Available Modules
Links
Boost
Mahuika
Maui
Maui_ancil
Boost provides free peer-reviewed portable C++ source libraries.
Available Modules
module load Boost/1.83.0-GCC-12.3.0
module load Boost/1.73.0-CrayIntel-23.02-19
module load Boost/1.77.0-GCC-9.2.0
Links
Bowtie
Biology
Mahuika
Ultrafast, memory-efficient short read aligner.
Available Modules
module load Bowtie/1.3.1-GCC-11.3.0
Links
Bowtie2
Biology
Mahuika
Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Available Modules
module load Bowtie2/2.4.5-GCC-11.3.0
Links
Bpipe
Biology
Mahuika
A platform for running big bioinformatics jobs that consist of a series of processing stages
Links
Bracken
Mahuika
Hghly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Available Modules
Links
BreakSeq2
Mahuika
Nucleotide-resolution analysis of structural variants
Available Modules
Links
CCL
Mahuika
Clozure CL (often called CCL for short) is a free Common Lisp implementation
Available Modules
Links
CD-HIT
Biology
Mahuika
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
Available Modules
Links
CDO
Climate_science
Mahuika
Maui_ancil
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
Available Modules
module load CDO/2.1.1-gimpi-2022a
module load CDO/2.0.5-GCC-7.1.0
Links
CFITSIO
Mahuika
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
Available Modules
Links
CGAL
Mahuika
The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
Available Modules
module load CGAL/5.5.2-GCC-11.3.0
Links
CMake
Mahuika
Maui
Maui_ancil
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
Available Modules
module load CMake/3.22.1
module load CMake/3.24.2
Links
CNVnator
Biology
Mahuika
Copy Number Variation discovery and genotyping from depth of read mapping.
Available Modules
Links
CNVpytor
Mahuika
Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped read
Available Modules
module load CNVpytor/1.3.1-gimkl-2022a-Python-3.11.3
Links
COMSOL
Chemistry
Engineering
Physics
Cae
Multiphysics
Cfd
Fea
Mahuika
COMSOL is a multiphysics solver that provides a unified workflow for electrical, mechanical, fluid, and chemical applications.
Licence
COMSOL is proprietary software.
Access to a valid licence token is required to run COMSOL.
Institution | Faculty | Uptime | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
University of Auckland | Physics | 98% | |||||||||
Auckland Bioengineering Institute | Implantable devices group | 98% | |||||||||
University of Auckland | Faculty of Engineering | 98% | |||||||||
University of Auckland | Deptartment of Engineering Science | 98% | |||||||||
University of Auckland | Deptartment of Engineering Science | 98% | |||||||||
|
|||||||||||
University of Otago | 99% | ||||||||||
University of Canterbury | 100% |
CONCOCT
Mahuika
Program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
Available Modules
module load CONCOCT/1.1.0-gimkl-2020a-Python-3.8.2
Links
CP2K
Chemistry
Mahuika
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
Available Modules
module load CP2K/8.2-intel-2022a-PLUMED-2.7.2
Links
CPMD
Mahuika
The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.
Available Modules
Links
CRAMINO
Mahuika
A tool for quick quality assessment of cram and bam files, intended for long read sequencing
Available Modules
Links
CTPL
Mahuika
C++ Thread Pool Library
Available Modules
Links
CUDA
Mahuika
Maui_ancil
CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
CUnit
Mahuika
Automated testing framework for C.
Available Modules
Links
Canu
Biology
Mahuika
Sequence assembler designed for high-noise single-molecule sequencing.
Available Modules
Links
CapnProto
Mahuika
Fast data interchange format and capability-based RPC system.
Available Modules
module load CapnProto/1.0.2-GCC-12.3.0
Links
Catch2
Mahuika
A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)
Available Modules
Links
CellRanger
Mahuika
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
Links
Centrifuge
Mahuika
Classifier for metagenomic sequences
Available Modules
module load Centrifuge/1.0.4-GCCcore-9.2.0
Links
Cereal
Mahuika
C++11 serialization library
Available Modules
Links
Charm++
Maui
An asynchronous message-driven C++ communication library targeted towards tightly coupled, high-performance parallel machines.
Available Modules
module load Charm++/6.8.0-CrayIntel-23.02-19
Links
CheckM
Mahuika
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Available Modules
module load CheckM/1.2.1-gimkl-2022a-Python-3.10.5
Links
CheckM2
Mahuika
Rapid assessment of genome bin quality using machine learning
Available Modules
Links
CheckV
Mahuika
Assess the quality of metagenome-assembled viral genomes.
Available Modules
module load CheckV/1.0.1-gimkl-2022a-Python-3.10.5
Links
Circlator
Mahuika
A tool to circularize genome assemblies
Available Modules
Links
Circos
Mahuika
Package for visualizing data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
Available Modules
Links
Clair3
Mahuika
Syumphonizing pileup and full-alignment for high-performance long-read variant calling.
Available Modules
Clang
Mahuika
C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
Available Modules
Links
Clustal-Omega
Biology
Mahuika
Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
Available Modules
Links
ClustalW2
Mahuika
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
Available Modules
Links
Corset
Mahuika
Clusters contigs and counts reads from de novo assembled transcriptomes.
Available Modules
Links
CoverM
Mahuika
DNA read coverage and relative abundance calculator focused on metagenomics applications
Available Modules
Links
CppUnit
Mahuika
C++ port of the JUnit framework for unit testing.
Available Modules
Links
CrayCCE
Maui
Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: February 2023).
Available Modules
Links
CrayGNU
Maui
Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: 23.02).
Available Modules
Links
CrayIntel
Maui
Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: February 2023 with Intel 19 compiler).
Available Modules
Links
CubeGUI
Mahuika
Graphical report explorer report explorer for Scalasca and Score-P
Available Modules
Links
CubeLib
Mahuika
Cube general purpose C++ library component and command-line tools.
Available Modules
Links
CubeWriter
Mahuika
Cube high-performance C writer library component.
Available Modules
Links
Cufflinks
Biology
Mahuika
Transcript assembly, differential expression, and differential regulation for RNA-Seq
Available Modules
Links
Cytoscape
Biology
Visualisation
Mahuika
Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Links
D-Genies
Mahuika
D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.
Available Modules
module load D-Genies/1.5.0-gimkl-2022a-Python-3.11.3
Links
DAS_Tool
Mahuika
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Available Modules
Links
DB
Mahuika
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
Available Modules
Links
DBus
Mahuika
D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
Available Modules
Links
DFT-D4
Mahuika
Generally Applicable Atomic-Charge Dependent London Dispersion Correction.
Available Modules
Links
DIAMOND
Biology
Mahuika
Sequence aligner for protein and translated DNA searches
Available Modules
module load DIAMOND/2.1.9-GCC-11.3.0
Links
DISCOVARdenovo
Mahuika
Assembler suitable for large genomes based on Illumina reads of length 250 or longer.
Available Modules
Links
DRAM
Mahuika
Tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs..
Available Modules
Links
DaliLite
Mahuika
Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
Available Modules
Links
DeconSeq
Mahuika
A tool that can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.
Available Modules
Links
DeePMD-kit
Mahuika
Available Modules
Links
DeepLabCut
Mahuika
Efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks.
Links
DefaultModules
Mahuika
Defines the set of modules loaded by default
Available Modules
module load DefaultModules/
Links
Delft3D
Hydrodynamics
Mahuika
Integrated simulation of sediment transport and morphology, waves, water quality and ecology.
Available Modules
Delft3D_FM
Mahuika
3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments
Available Modules
Links
Delly
Mahuika
Structural variant discovery by integrated paired-end and split-read analysis
Links
Dorado
Mahuika
Doxygen
Mahuika
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
Available Modules
Links
Dsuite
Mahuika
Fast calculation of the ABBA-BABA statistics across many populations/species
Available Modules
Links
EDTA
Mahuika
Automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.
Links
EIGENSOFT
Mahuika
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
Available Modules
Links
ELPA
Mahuika
Eigenvalue SoLvers for Petaflop-Applications .
Available Modules
module load ELPA/2023.11.001-foss-2023a
Links
EMAN2
Mahuika
Greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes
Available Modules
Links
EMBOSS
Biology
Mahuika
EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
Available Modules
Links
ENMTML
Mahuika
R package for integrated construction of Ecological Niche Models.
Available Modules
Links
ESMF
Climate_science
Earth_science
Mahuika
Maui
Maui_ancil
The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.
Available Modules
module load ESMF/7.1.0r-intel-2018b
module load ESMF/8.4.2-CrayIntel-23.02-19
module load ESMF/7.1.0r-intel-2018b
Links
ETE
Mahuika
A Python framework for the analysis and visualization of phylogenetic trees
Available Modules
module load ETE/3.1.2-gimkl-2022a-Python-3.10.5
Links
EasyBuild
Mahuika
Maui
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
Eigen
Mathematics
Mahuika
Embree
Mahuika
Maui_ancil
Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels.
Available Modules
module load Embree/3.12.2-GCCcore-9.2.0
module load Embree/3.2.0-GCC-7.1.0
Links
EukRep-EukCC
Mahuika
Completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. Also condatains smetana, carveme and memote .
Available Modules
Links
ExaBayes
Biology
Mahuika
Bayesian tree inference, particularly suitable for large-scale analyses.
Available Modules
Links
ExaML
Biology
Mahuika
Exascale Maximum Likelihood for phylogenetic inference using MPI.
Available Modules
Links
ExpansionHunter
Mahuika
Tool for estimating repeat sizes
Available Modules
Links
Extrae
Mahuika
Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches
Available Modules
Links
FALCON
Biology
Mahuika
Falcon: a set of tools for fast aligning long reads for consensus and assembly
Available Modules
Links
FASTX-Toolkit
Biology
Mahuika
Tools for Short-Reads FASTA/FASTQ files preprocessing.
Available Modules
Links
FCM
Maui
Maui_ancil
FCM Build - A powerful build system for modern Fortran software applications. FCM Version Control - Wrappers to the Subversion version control system, usage conventions and processes for scientific software development.
Available Modules
module load FCM/2019.09.0
module load FCM/2019.09.0-GCC-9.2.0
Links
FDS
Engineering
Physics
Mahuika
Mahuika
Maui
Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.
Available Modules
module load FDS/6.7.9-intel-2022a
module load FDS/6.7.1-CrayIntel-23.02-19
FFTW
Mahuika
Maui
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
Available Modules
module load FFTW/3.3.10-gompi-2022a
module load FFTW/3.3.9-CrayIntel-23.02-19
Links
FFTW.MPI
Mahuika
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
Available Modules
Links
FFmpeg
Mahuika
Maui_ancil
A complete, cross-platform solution to record, convert and stream audio and video.
Available Modules
module load FFmpeg/5.1.1-GCC-11.3.0
module load FFmpeg/3.4.2-GCC-7.1.0
Links
FIGARO
Mahuika
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.
Available Modules
Links
FLTK
Mahuika
FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
Available Modules
Links
FTGL
Mahuika
Maui_ancil
FTGL is a free cross-platform Open Source C++ library that uses Freetype2 to simplify rendering fonts in OpenGL applications. FTGL supports bitmaps, pixmaps, texture maps, outlines, polygon mesh, and extruded polygon rendering modes.
Available Modules
module load FTGL/2.1.3-rc5-GCCcore-7.4.0
module load FTGL/2.1.3-rc5-GCC-7.1.0
Links
FastANI
Mahuika
Tool for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
Available Modules
module load FastANI/1.33-intel-2022a
Links
FastME
Mahuika
FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.
Available Modules
Links
FastQC
Biology
Mahuika
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
Links
FastQ_Screen
Mahuika
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Available Modules
Links
FastTree
Biology
Mahuika
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
Available Modules
module load FastTree/2.1.11-GCCcore-9.2.0
Links
File-Rename
Mahuika
A Perl version of the rename utility, with support for regular expressions.
Available Modules
Links
Filtlong
Mahuika
Tool for filtering long reads by quality.
Available Modules
Links
FimTyper
Mahuika
Identifies the FimH type in total or partial sequenced isolates of E. coli..
Available Modules
Links
FlexiBLAS
Mahuika
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
Available Modules
Flye
Biology
Mahuika
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.
Available Modules
module load Flye/2.9.3-gimkl-2022a-Python-3.11.3
Links
FragGeneScan
Mahuika
FragGeneScan is an application for finding (fragmented) genes in short reads.
Available Modules
Links
FreeBayes
Biology
Mahuika
Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.
Available Modules
Links
FreeSurfer
Mahuika
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.
Available Modules
Links
FreeXL
Mahuika
FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
Available Modules
module load FreeXL/1.0.5-GCCcore-11.3.0
Links
FriBidi
Mahuika
Free Implementation of the Unicode Bidirectional Algorithm.
Available Modules
Links
GATK
Biology
Mahuika
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Available Modules
GCC
Mahuika
Maui_ancil
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GCCcore
Mahuika
Maui_ancil
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GD
Mahuika
Interface to Gd Graphics Library
Available Modules
Links
GDAL
Earth_science
Mahuika
Maui
Maui_ancil
GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.
Available Modules
module load GDAL/3.6.4-gompi-2023a
module load GDAL/3.0.4-CrayIntel-23.02-19
module load GDAL/3.6.4-gimpi-2020a
Links
GEMMA
Mahuika
Genome-wide Efficient Mixed Model Association
Available Modules
Links
GEOS
Mathematics
Mahuika
Maui_ancil
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
Available Modules
module load GEOS/3.11.3-GCC-12.3.0
module load GEOS/3.9.1-GCC-9.2.0
Links
GLM
Mahuika
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
Available Modules
Links
GLPK
Mahuika
GNU Linear Programming Kit is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.
Available Modules
Links
GLib
Mahuika
Maui_ancil
GLib is one of the base libraries of the GTK+ project
Available Modules
module load GLib/2.72.1-GCC-11.3.0
module load GLib/2.53.1-GCC-7.1.0
Links
GMAP-GSNAP
Biology
Mahuika
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
Available Modules
Links
GMP
Mathematics
Mahuika
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
Available Modules
module load GMP/6.2.1-GCCcore-12.3.0
Links
GMT
Maui_ancil
GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
Available Modules
Links
GOLD
Mahuika
A genetic algorithm for docking flexible ligands into protein binding sites
Links
Licence
GOLD is proprietary software.
GObject-Introspection
Mahuika
GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
Available Modules
GPAW
Mahuika
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.
Available Modules
Links
GRADS
Maui_ancil
The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.
Available Modules
Links
GRASS
Earth_science
Visualisation
Mahuika
The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
Available Modules
Links
GRIDSS
Mahuika
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
Available Modules
Links
GROMACS
Chemistry
Mahuika
Maui
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Available Modules
module load GROMACS/2021.6-gimkl-2020a-cuda-11.6.2-hybrid-PLUMED-2.8.0
module load GROMACS/2023-CrayGNU-23.02
GSL
Mathematics
Mahuika
Maui_ancil
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
Available Modules
module load GSL/2.7-GCC-12.3.0
module load GSL/2.4-GCC-7.1.0
Links
GST-plugins-base
Mahuika
GStreamer plug-ins and elements.
Available Modules
GStreamer
Mahuika
Maui_ancil
GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
Available Modules
module load GStreamer/1.16.2-GCC-9.2.0
module load GStreamer/1.16.0-GCC-7.1.0
Links
GTDB-Tk
Mahuika
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Available Modules
module load GTDB-Tk/2.4.0-foss-2023a-Python-3.11.6
Links
GTK+
Mahuika
GTK+ is the primary library used to construct user interfaces in GNOME.
Available Modules
Links
GTS
Mahuika
Maui
Maui_ancil
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
Available Modules
module load GTS/121130-GCCcore-7.4.0
module load GTS/0.7.6-CrayGNU-23.02
module load GTS/121130-GCC-7.1.0
Links
GUSHR
Mahuika
Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.
Available Modules
module load GUSHR/2020-09-28-gimkl-2022a
Links
Gaussian
Chemistry
Mahuika
Mahuika
Links
Licence
Gaussian is proprietary software.
Gdk-Pixbuf
Mahuika
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
Available Modules
Links
GeneMark-ES
Mahuika
Eukaryotic gene prediction suite with automatic training
Available Modules
Links
GenoVi
Mahuika
Generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.
Available Modules
Links
GenomeThreader
Mahuika
GenomeThreader is a software tool to compute gene structure predictions.
Available Modules
Links
Gerris
Mahuika
Maui_ancil
Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow. This module also includes GfsView, a visualisation application for Gerris output.
Available Modules
module load Gerris/20180227-gimkl-2018b
module load Gerris/20180227-gimpi-2018b
Links
GetOrganelle
Mahuika
Toolkit to assemble organelle genome from genomic skimming data.
Available Modules
Links
GlimmerHMM
Mahuika
Gene finder based on a Generalized Hidden Markov Model.
Available Modules
Links
Go
Mahuika
Maui
Graphviz
Mahuika
Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Available Modules
Links
Gubbins
Biology
Mahuika
Genealogies Unbiased By recomBinations In Nucleotide Sequences
Available Modules
Links
Guile
Mahuika
Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
Available Modules
Links
HDF
Mahuika
Maui_ancil
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
Available Modules
module load HDF/4.2.16-GCC-12.3.0
module load HDF/4.2.13-iccifort-2018.1.163-GCC-7.1.0-fortran
Links
HDF-EOS
Maui_ancil
HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura.
Available Modules
Links
HDF-EOS5
Maui_ancil
HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura.
Available Modules
Links
HDF5
Mahuika
Maui_ancil
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
Available Modules
module load HDF5/1.14.3-gompi-2023a
module load HDF5/1.12.0-iccifort-2020.0.166
Links
HISAT2
Biology
Mahuika
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
Available Modules
module load HISAT2/2.2.1-gimpi-2022a
Links
HMMER
Biology
Mahuika
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
Available Modules
module load HMMER/3.3.2-GCC-12.3.0
Links
HMMER2
Mahuika
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
Available Modules
Links
HOPS
Mahuika
Pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.
Available Modules
Links
HTSeq
Mahuika
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
Available Modules
Links
HTSlib
Biology
Mahuika
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
Available Modules
Links
HarfBuzz
Mahuika
HarfBuzz is an OpenType text shaping engine.
Available Modules
Links
HpcGridRunner
Mahuika
HPC GridRunner is a simple command-line interface to high throughput computing using a variety of different grid computing platforms, including LSF, SGE, SLURM, and PBS.
Links
Humann
Mahuika
Pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.
Available Modules
Links
HybPiper
Mahuika
Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment.
Available Modules
Links
Hypre
Mahuika
Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
Available Modules
Links
ICU
Mahuika
Maui_ancil
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
Available Modules
module load ICU/71.1-GCC-11.3.0
module load ICU/62.1-GCC-7.1.0
Links
IDBA-UD
Mahuika
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
Available Modules
Links
IDL
Maui_ancil
IDL is the trusted scientific programming language used across disciplines to extract meaningful visualizations from complex numerical data.
Available Modules
Links
IGV
Biology
Visualisation
Mahuika
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data
Links
IMPUTE
Biology
Mahuika
Genotype imputation and haplotype phasing.
Available Modules
Links
IQ-TREE
Mahuika
Efficient phylogenomic software by maximum likelihood
Available Modules
module load IQ-TREE/2.2.2.2-gimpi-2022a
Links
IQmol
Visualisation
Mahuika
IRkernel
Mahuika
Maui_ancil
R packages for providing R kernel for Jupyter.
Available Modules
module load IRkernel/1.3.1-gimkl-2022a-R-4.2.1
module load IRkernel/1.0.1-gimkl-2018b
Links
ISA-L
Mahuika
Intelligent Storage Acceleration Library
Available Modules
Links
ImageMagick
Mahuika
Maui_ancil
ImageMagick is a software suite to create, edit, compose, or convert bitmap images
Available Modules
module load ImageMagick/7.0.9-5-GCCcore-9.2.0
module load ImageMagick/7.0.8-11-GCC-7.1.0
Links
Infernal
Biology
Mahuika
Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.
Available Modules
module load Infernal/1.1.4-GCC-11.3.0
Links
Inspector
Mahuika
Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications
Available Modules
Links
InterProScan
Mahuika
Sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.
Available Modules
module load InterProScan/5.66-98.0-gimkl-2022aPerl-5.34.1-Python-3.11.3
Links
JAGS
Mathematics
Mahuika
Just Another Gibbs Sampler - a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
Available Modules
module load JAGS/4.3.1-gimkl-2022a-mt
Links
JUnit
Mahuika
A programmer-oriented testing framework for Java.
Available Modules
Links
JasPer
Mahuika
Maui_ancil
The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
Available Modules
module load JasPer/2.0.33-GCC-12.3.0
module load JasPer/2.0.14-GCC-7.1.0
Links
Java
Language
Mahuika
General
Mahuika
Maui_ancil
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Available Modules
Jellyfish
Biology
Mahuika
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
Available Modules
module load Jellyfish/2.3.0-gimkl-2020a
Links
JsonCpp
Mahuika
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
Available Modules
Links
Julia
Mahuika
Maui_ancil
A high-level, high-performance dynamic language for technical computing. This version was compiled from source with USE_INTEL_JITEVENTS=1 to enable profiling with VTune.
Available Modules
module load Julia/1.9.4-GCC-11.3.0-VTune
module load Julia/1.7.1-GCC-9.2.0-VTune
JupyterLab
Mahuika
An extensible environment for interactive and reproducible computing, based on the Jupyter Notebook and Architecture.
Available Modules
module load JupyterLab/2023.11.0-gimkl-2022a-3.6.3
KAT
Mahuika
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
Available Modules
Links
KEALib
Mahuika
Maui_ancil
KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software.
Available Modules
module load KEALib/1.5.2-gompi-2023a
module load KEALib/1.4.15-gimpi-2020a
Links
KMC
Mahuika
Disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.
Available Modules
module load KMC/3.1.2rc1-gimkl-2020a-Python-3.8.2
Links
Kaiju
Mahuika
Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments
Available Modules
module load Kaiju/1.8.2-gimkl-2020a-Python-3.9.9-Perl-5.30.1-mt
Links
Kent_tools
Mahuika
Collection of tools used by the UCSC genome browser.
Available Modules
Links
KmerGenie
Mahuika
KmerGenie estimates the best k-mer length for genome de novo assembly.
Available Modules
Links
KorfSNAP
Mahuika
Semi-HMM-based Nucleic Acid Parser
Available Modules
Links
Kraken2
Biology
Mahuika
Taxonomic sequence classifier.
Available Modules
module load Kraken2/2.1.3-GCC-11.3.0
Links
KronaTools
Mahuika
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
Available Modules
Links
KyotoCabinet
Mahuika
Library of routines for managing a database.
Available Modules
Links
LAME
Mahuika
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
Available Modules
Links
LAMMPS
Biology
Chemistry
Mahuika
Maui
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
Available Modules
module load LAMMPS/20180316-gimkl-2017a
module load LAMMPS/20190430-CrayIntel-23.02-19
Links
LAST
Mahuika
LAST finds similar regions between sequences.
Available Modules
Links
LASTZ
Biology
Mahuika
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
Available Modules
Links
LDC
Language
Mahuika
D programming language compiler
Links
LEfSe
Mahuika
Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance
Available Modules
Links
LINKS
Mahuika
Alignment-free scaffolding of genome assembly drafts with long reads
Available Modules
Links
LLVM
Mahuika
Maui_ancil
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. This build includes the clang C/C++ compiler frontend.
Available Modules
module load LLVM/14.0.6-GCC-12.3.0-static
module load LLVM/6.0.1-GCC-7.1.0
Links
LMDB
Mahuika
LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
Available Modules
module load LMDB/0.9.31-GCC-12.3.0
Links
LSD2
Mahuika
Least-squares methods to estimate rates and dates from phylogenies
Available Modules
Links
LTR_retriever
Mahuika
Highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
Available Modules
Links
LUMPY
Mahuika
A probabilistic framework for structural variant discovery.
Available Modules
Links
LZO
Mahuika
Portable lossless data compression library
Available Modules
Links
LegacySystemLibs
Mahuika
Available Modules
Links
LibTIFF
Mahuika
Maui
Maui_ancil
tiff: Library and tools for reading and writing TIFF data files
Available Modules
module load LibTIFF/4.5.1-GCCcore-12.3.0
module load LibTIFF/4.3.0-CrayIntel-23.02-19
module load LibTIFF/4.4.0-GCCcore-9.2.0
Links
Libint
Chemistry
Mahuika
Maui
Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
Available Modules
module load Libint/2.6.0-iimpi-2022a-lmax-6-cp2k
module load Libint/1.1.6-CrayGNU-23.02
Links
Liftoff
Mahuika
Tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.
Available Modules
Links
LittleCMS
Mahuika
Color management engine.
Available Modules
Links
LongStitch
Mahuika
A genome assembly correction and scaffolding pipeline using long reads
Available Modules
Links
M4
Mahuika
GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
Available Modules
Links
MAFFT
Biology
Mahuika
Multiple sequence alignment program offering a range of methods.
Available Modules
module load MAFFT/7.505-gimkl-2022a-with-extensions
Links
MAGMA
Mahuika
Tool for gene analysis and generalized gene-set analysis of GWAS data.
Available Modules
Links
MAKER
Mahuika
Genome annotation pipeline
Available Modules
MATIO
Mahuika
matio is an C library for reading and writing Matlab MAT files.
Available Modules
Links
MATLAB
Engineering
Mathematics
Visualisation
Ml
Mahuika
Maui_ancil
A high-level language and interactive environment for numerical computing.
Available Modules
Licence
MATLAB is proprietary software.
Access to a valid licence token is required to run MATLAB.
Institution | Uptime |
---|---|
University of Waikato | 99% |
National Institute of Water and Atmospheric Research | 0% |
Institute of Geological and Nuclear Sciences | 99% |
Massey University | 36% |
University of Auckland | 98% |
University of Otago | 100% |
Victoria University of Wellington | 100% |
Auckland University of Technology | 35% |
University of Canterbury | 35% |
Plant & Food Research | 36% |
MCL
Mahuika
The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.
Available Modules
Links
MCR
Mahuika
Maui_ancil
MEGAHIT
Mahuika
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Available Modules
module load MEGAHIT/1.2.9-gimkl-2022a-Python-3.10.5
Links
METABOLIC
Mahuika
Metabolic And Biogeochemistry anaLyses In microbes
Available Modules
Links
METIS
Mathematics
Mahuika
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
Available Modules
module load METIS/5.1.0-intel-2022a
Links
MMseqs2
Mahuika
MMseqs2: ultra fast and sensitive search and clustering suite
Available Modules
module load MMseqs2/15-6f452-gompi-2023a
Links
MOB-suite
Mahuika
Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
Available Modules
Links
MODFLOW
Mahuika
MODFLOW is the U.S. Geological Survey modular finite-difference flow model, which is a computer code that solves the groundwater flow equation. The program is used by hydrogeologists to simulate the flow of groundwater through aquifers.
Available Modules
Links
MPFR
Mathematics
Mahuika
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
Available Modules
module load MPFR/4.1.0-GCC-11.3.0
Links
MSMC
Mahuika
Multiple Sequentially Markovian Coalescent, infers population size and gene flow from multiple genome sequences
Available Modules
Links
MUMPS
Mathematics
Mahuika
A parallel sparse direct solver
Available Modules
module load MUMPS/5.6.1-foss-2023a
Links
MUMmer
Biology
Mahuika
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
Available Modules
module load MUMmer/4.0.0rc1-GCCcore-11.3.0
Links
MUSCLE
Biology
Mahuika
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.
Links
MUST
Mahuika
MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user.
Available Modules
Links
MaSuRCA
Biology
Mahuika
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).
Available Modules
module load MaSuRCA/4.1.0-GCC-11.3.0
Links
Magma
Mahuika
Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. It provides a mathematically rigorous environment for defining and working with structures such as groups, rings, fields, modules, algebras, schemes, curves, graphs, designs, codes and many others. Magma also supports a number of databases designed to aid computational research in those areas of mathematics which are algebraic in nature. whatis([==[Homepage: http://magma.maths.usyd.edu.au/magma/
Available Modules
Links
Mamba
Mahuika
Mamba is a fast, robust, and cross-platform package manager.
Available Modules
Links
MarkerMiner
Mahuika
Workflow for effective discovery of SCN loci in flowering plants angiosperms
Available Modules
Links
Mash
Mahuika
Fast genome and metagenome distance estimation using MinHash
Available Modules
module load Mash/2.3-GCC-12.3.0
Links
MashMap
Mahuika
Implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences
Available Modules
Links
Maven
Mahuika
Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
Available Modules
Links
MaxBin
Mahuika
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
Available Modules
module load MaxBin/2.2.7-GCC-11.3.0-Perl-5.34.1
Links
Merqury
Mahuika
Evaluate genome assemblies with k-mers and more
Available Modules
Links
Mesa
Visualisation
Mahuika
Maui_ancil
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Note that this build enables CPU-based rendering with OpenSWR and LLVM. The module is intended to be used with visualisation software, such as ParaView, on nodes where no GPU hardware is available. Both on-screen and off-screen rendering are supported. IMPORTANT: The OpenSWR software rasteriser can use multiple threads for best performance. The number of threads is controlled by the environment variable KNOB_MAX_WORKER_THREADS. The module sets KNOB_MAX_WORKER_THREADS=1 by default to avoid accidental oversubscription of nodes.
Available Modules
module load Mesa/19.2.1-GCCcore-9.2.0
module load Mesa/18.1.8-GCC-7.1.0
Links
Meson
Mahuika
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
Links
MetaBAT
Mahuika
An efficient tool for accurately reconstructing single genomes from complex microbial communities
Available Modules
Links
MetaEuk
Mahuika
MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
Available Modules
Links
MetaGeneAnnotator
Mahuika
MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
Available Modules
MetaPhlAn
Mahuika
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
Available Modules
module load MetaPhlAn/4.1.0-gimkl-2022a-Python-3.10.5
Links
MetaPhlAn2
Mahuika
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
Available Modules
Links
MetaSV
Mahuika
Structural-variant caller
Available Modules
Links
Metashape
Mahuika
Available Modules
Links
Metaxa2
Biology
Mahuika
Taxonomic classification of rRNA.
Available Modules
Links
MiMiC
Mahuika
Available Modules
Links
MiMiC-CommLib
Mahuika
The MiMiC communication library (MCL) enables communication between external programs coupled through the MiMiC framework.
Available Modules
Links
Miniconda3
Language
Mahuika
Maui
Maui_ancil
A platform for Python-based data analytics
Minimac3
Mahuika
Low memory and more computationally efficient implementation of the genotype imputation algorithms.
Available Modules
Links
Minimac4
Mahuika
Low memory and more computationally efficient implementation of the genotype imputation algorithms.
Available Modules
Links
MitoZ
Mahuika
Toolkit which aims to automatically filter pair-end raw data, assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome, and mitogenome visualization.
Available Modules
module load MitoZ/2.3-gimkl-2020a-Python-3.8.2
Links
ModDotPlot
Mahuika
Novel dot plot visualization tool used to view tandem repeats
Available Modules
Links
ModelTest-NG
Mahuika
Tool for selecting the best-fit model of evolution for DNA and protein alignments.
Available Modules
Links
Molcas
Chemistry
Mahuika
Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.
Available Modules
Links
Molpro
Chemistry
Mahuika
Tier1
Mahuika
Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
Available Modules
module load Molpro/mpp-2019.2.2.linux_x86_64_openmp
Mono
Mahuika
An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
Available Modules
Links
Monocle3
Mahuika
An analysis toolkit for single-cell RNA-seq.
Available Modules
Links
Mothur
Biology
Mahuika
Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
Available Modules
Links
MrBayes
Biology
Mahuika
MrBayes is a program for the Bayesian estimation of phylogeny.
Available Modules
Links
Mule
Maui_ancil
Mule is an API written in Python which allows you to access and manipulate files produced by the UM (Unified Model, of the Met Office (UK)).
Available Modules
module load Mule/2022.05.1-GCC-9.2.0-Miniconda3-22.11.1
Links
MultiQC
Biology
Mahuika
Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
Available Modules
module load MultiQC/1.13-gimkl-2022a-Python-3.10.5
Links
NAMD
Biology
Chemistry
Mahuika
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Available Modules
module load NAMD/2.14-gimkl-2022a-mpi
Links
NASM
Language
Mahuika
Maui
Maui_ancil
NASM: General-purpose x86 assembler
Available Modules
module load NASM/2.15.05
module load NASM/2.14.02-CrayGNU-23.02
module load NASM/2.15.05
Links
NCCL
Mahuika
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
Available Modules
module load NCCL/2.17.1-CUDA-12.0.0
Links
NCL
Visualisation
Mahuika
Maui_ancil
NCL is an interpreted language designed specifically for scientific data analysis and visualization.
Available Modules
module load NCL/6.6.2-intel-2018b
module load NCL/6.4.0-GCC-7.1.0
Links
NCO
Mahuika
Maui_ancil
manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
Available Modules
module load NCO/4.8.1-gimpi-2022a
module load NCO/4.8.1-GCC-7.1.0
Links
NCVIEW
Maui_ancil
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
Available Modules
Links
NECAT
Mahuika
Rrror correction and de-novo assembly tool for Nanopore long noisy reads
Available Modules
Links
NGS
Biology
Mahuika
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
Available Modules
module load NGS/2.11.2-GCC-11.3.0
Links
NLopt
Mahuika
Maui_ancil
NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms
Available Modules
module load NLopt/2.7.1-GCC-12.3.0
module load NLopt/2.5.0-gimkl-2018b
Links
NONMEM
Mahuika
Available Modules
Links
NSPR
Mahuika
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
Available Modules
Links
NSS
Mahuika
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
Available Modules
Links
NVHPC
Mahuika
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
Available Modules
module load NVHPC/23.5-CUDA-12.1.1
Links
NWChem
Biology
Chemistry
Mahuika
Tier1
Mahuika
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.
Available Modules
module load NWChem/6.8.1.revision133-gimkl-2018b-2018-06-14-Python-2.7.16
NanoComp
Mahuika
Comparing runs of Oxford Nanopore sequencing data and alignments
Available Modules
Links
NanoLyse
Mahuika
Removing reads mapping to the lambda genome.
Available Modules
Links
NanoPlot
Mahuika
Plotting suite for Oxford Nanopore sequencing data and alignments.
Available Modules
module load NanoPlot/1.41.0-gimkl-2022a-Python-3.10.5
Links
NanoStat
Mahuika
Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.
Available Modules
Links
NewHybrids
Mahuika
This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.
Available Modules
Links
Newton-X
Mahuika
NX is a general-purpose program package for simulating the dynamics of electronically excited molecules and molecular assemblies.
Available Modules
Links
NextGenMap
Mahuika
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.
Available Modules
Links
Nextflow
Workflow_management
Mahuika
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
Nim
Mahuika
Nim is a systems and applications programming language.
Available Modules
Links
Ninja
Mahuika
Ninja is a small build system with a focus on speed.
Links
Nsight-Compute
Mahuika
NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and command line tool.
Available Modules
Links
Nsight-Systems
Mahuika
NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs
Available Modules
Links
OASIS3-MCT
Maui
The OASIS coupler is a software allowing synchronized exchanges of coupling information between numerical codes representing different components of the climate system.
Available Modules
module load OASIS3-MCT/r1660-CrayIntel-23.02-19
Links
OBITools
Mahuika
Manipulate various data and sequence files.
Available Modules
Links
OCI
Maui_ancil
Oracle Call Interface (OCI) is the comprehensive, high performance, native C language interface to Oracle Database for custom or packaged applications. NOTE: This package is only available on Maui Ancil nodes that provide database access.
Available Modules
Links
OMA
Mahuika
Orthologous MAtrix project is a method and database for the inference of orthologs among complete genomes
Available Modules
Links
OPARI2
Mahuika
source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
Available Modules
Links
ORCA
Chemistry
Mahuika
Mahuika
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
Available Modules
module load ORCA/5.0.4-OpenMPI-4.1.5
OSPRay
Visualisation
Mahuika
Maui_ancil
OSPRay features interactive CPU rendering capabilities geared towards Scientific Visualization applications. Advanced shading effects such as Ambient Occlusion, shadows, and transparency can be rendered interactively, enabling new insights into data exploration.
Available Modules
module load OSPRay/1.8.2-GCCcore-7.4.0
module load OSPRay/1.6.1-GCC-7.1.0
Links
OSU-Micro-Benchmarks
Mahuika
Maui
OSU Micro-Benchmarks for MPI
Available Modules
module load OSU-Micro-Benchmarks/6.2-gompi-2022a
module load OSU-Micro-Benchmarks/6.2-CrayIntel-23.02-19
OTF2
Mahuika
The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library
Available Modules
Links
Octave
Engineering
Mathematics
Mahuika
GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
Available Modules
Links
OpenBLAS
Mahuika
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
Available Modules
module load OpenBLAS/0.3.23-GCC-12.3.0
Links
OpenBabel
Biology
Chemistry
Mahuika
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Available Modules
Links
OpenCV
Machine_learning
Mahuika
OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
Available Modules
Links
OpenFAST
Engineering
Physics
Mahuika
Wind turbine multiphysics simulation tool
Available Modules
Links
OpenFOAM
Chemistry
Engineering
Cfd
Cae
Fea
Mahuika
OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
Available Modules
OpenJPEG
Mahuika
Maui_ancil
An open-source JPEG 2000 codec written in C
Available Modules
module load OpenJPEG/2.5.0-GCCcore-12.3.0
module load OpenJPEG/2.5.0-GCCcore-9.2.0
Links
OpenMPI
Mahuika
The Open MPI Project is an open source MPI-3 implementation.
Available Modules
module load OpenMPI/4.1.5-GCC-12.3.0
Links
OpenSSL
Mahuika
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
Available Modules
module load OpenSSL/1.1.1k-GCCcore-12.3.0
Links
OpenSees
Earth_science
Engineering
Geo
Earthquake
Mahuika
OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes.
Available Modules
module load OpenSees/20220411-gimkl-2020a
OpenSeesPy
Mahuika
OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes.
Available Modules
Links
OpenSlide
Mahuika
OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
Available Modules
Links
OrfM
Mahuika
A simple and not slow open reading frame (ORF) caller.
Available Modules
Links
OrthoFiller
Mahuika
Identifies missing annotations for evolutionarily conserved genes.
Available Modules
Links
OrthoFinder
Mahuika
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics
Available Modules
module load OrthoFinder/2.5.2-gimkl-2020a-Python-3.8.2
Links
OrthoMCL
Mahuika
Genome-scale algorithm for grouping orthologous protein sequences.
Available Modules
Links
PALEOMIX
Mahuika
pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.
Available Modules
Links
PAML
Mahuika
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Available Modules
Links
PAPI
Mahuika
PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
Available Modules
Links
PCRE
Mahuika
Maui_ancil
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
Available Modules
module load PCRE/8.45-GCC-11.3.0
module load PCRE/8.43-GCCcore-7.1.0
Links
PCRE2
Mahuika
Maui_ancil
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
Available Modules
module load PCRE2/10.42-GCCcore-12.3.0
module load PCRE2/10.40-GCCcore-9.2.0
Links
PDT
Mahuika
Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools.
Available Modules
Links
PEAR
Mahuika
Memory-efficient,fully parallelized and highly accurate pair-end read merger.
Available Modules
Links
PEST++
Mahuika
PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model.
Available Modules
Links
PETSc
Mahuika
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
Available Modules
Links
PHASIUS
Mahuika
A tool to visualize phase block structure from (many) BAM or CRAM files together with BED annotation
Available Modules
Links
PLINK
Biology
Mahuika
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
Links
PLUMED
Biology
Chemistry
Mahuika
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
Available Modules
module load PLUMED/2.8.0-intel-2020a
Links
PRANK
Mahuika
Probabilistic multiple alignment program for DNA, codon and amino-acid sequences. .
Available Modules
Links
PROJ
Mahuika
Maui
Maui_ancil
Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
Available Modules
module load PROJ/9.3.0-GCC-12.3.0
module load PROJ/8.1.1-CrayIntel-23.02-19
module load PROJ/9.1.1-GCC-9.2.0
Links
PSpaMM
Mahuika
Generates inline-Assembly for sparse Matrix Multiplication.
Available Modules
Links
PUMI
Mahuika
parallel unstructured mesh infrastructure API
Available Modules
Links
Pango
Mahuika
Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
Available Modules
Links
ParMETIS
Mathematics
Mahuika
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
Available Modules
module load ParMETIS/4.0.3-gimpi-2022a
Links
ParaView
Engineering
Visualisation
Mahuika
Maui_ancil
ParaView is a scientific parallel visualizer. This version supports CPU-only rendering without X context using the OSMesa library, it does not support GPU rendering, and it does not provide a GUI. Use the GALLIUM_DRIVER environment variable to choose a software renderer, it is recommended to use GALLIUM_DRIVER=swr for best performance. Ray tracing using the OSPRay library is also supported.
Available Modules
module load ParaView/5.9.0-gimkl-2020a-Python-3.8.2
module load ParaView/5.5.2-gimpi-2018b-Server-OSMesa
Parallel
Mahuika
Maui_ancil
ParallelIO
Mahuika
A high-level Parallel I/O Library for structured grid applications
Available Modules
Links
Paraver
Mahuika
Performance visualization and analysis tool based on traces.
Available Modules
Links
Peregrine
Mahuika
Genome assembler for long reads (length > 10kb, accuracy > 99%). Based on Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping
Available Modules
Links
Perl
Language
Mahuika
Maui_ancil
Larry Wall's Practical Extraction and Report Language
Available Modules
module load Perl/5.38.2-GCC-12.3.0
module load Perl/5.24.1-GCC-7.1.0
Links
PhyML
Biology
Mahuika
Phylogenetic estimation using Maximum Likelihood
Available Modules
Links
PhyloPhlAn
Mahuika
Integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
Available Modules
module load PhyloPhlAn/3.0.3-gimkl-2022a-Python-3.10.5
Links
Pilon
Biology
Mahuika
Pilon is an automated genome assembly improvement and variant detection tool
Available Modules
Links
PnetCDF
Mahuika
Parallel netCDF: A Parallel I/O Library for NetCDF File Access
Available Modules
Links
Porechop
Biology
Mahuika
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity
Available Modules
module load Porechop/0.2.4-gimkl-2022a-Python-3.11.3
Links
PostgreSQL
Mahuika
Maui_ancil
Client-side programs and libraries for accessing PostgreSQL databases.
Available Modules
module load PostgreSQL/12.2-gimkl-2020a-PostGIS-3.1.1
module load PostgreSQL/11.0-GCC-7.1.0
Links
Prodigal
Mahuika
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
Available Modules
Links
ProtHint
Mahuika
Pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.
Available Modules
module load ProtHint/2.6.0-gimkl-2022a-Perl-5.34.1-Python-3.11.3
Links
Proteinortho
Mahuika
Proteinortho is a tool to detect orthologous genes within different species.
Available Modules
module load Proteinortho/6.0.28-gimkl-2020a-Python-3.8.2-Perl-5.30.1
Links
PyOpenGL
Mahuika
PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.
Available Modules
Links
PyQt
Mahuika
PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.
Available Modules
module load PyQt/5.12.1-gimkl-2020a-Python-3.8.2
Links
PyTorch
Mahuika
Tensors and Dynamic neural networks in Python with strong GPU acceleration.
Available Modules
module load PyTorch/1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2
Links
Python
Data_analytics
Language
Machine_learning
Visualisation
Ml
Mahuika
Maui
Maui_ancil
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Available Modules
module load Python/3.11.6-foss-2023a
module load Python/3.8.2-CrayIntel-23.02-19
module load Python/3.8.2
Python-Geo
Earth_science
Mahuika
Python packages for geospatial data I/O, mostly based on the OSGEO libraries GDAL and OGR
Available Modules
module load Python-Geo/3.11.3-gimkl-2022a
Links
QChem
Chemistry
Mahuika
QIIME2
Biology
Mahuika
QUAST
Biology
Mahuika
Evaluates genome assemblies
Available Modules
Links
Qt5
Mahuika
Maui_ancil
Qt is a comprehensive cross-platform C++ application framework.
Available Modules
module load Qt5/5.13.2-GCCcore-9.2.0
module load Qt5/5.9.3-GCC-7.1.0
Links
QuantumESPRESSO
Chemistry
Mahuika
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
Available Modules
Links
QuickTree
Mahuika
Efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments .
Available Modules
Links
R
Data_analytics
Language
Machine_learning
Visualisation
Mahuika
R
Mahuika
Maui_ancil
R is a free software environment for statistical computing and graphics.
Available Modules
module load R/4.3.2-foss-2023a
module load R/3.6.1-gimkl-2018b
Links
R-Geo
Mahuika
R packages for Geometric and Geospatial data which depend on GEOS and/or GDAL.
Available Modules
module load R-Geo/4.3.2-foss-2023a
Links
R-bundle-Bioconductor
Mahuika
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
Available Modules
module load R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1
RANGS-GSHHS
Mahuika
Maui
A binary file set RANGS (Regionally Accessible Nested Global Shorelines) based on GSHHS (Global Self-consistent Hierarchical High-resolution Shorelines) data. Note: RANGS-GSHHS is used with NCL.
Available Modules
Links
RAxML
Biology
Mahuika
Mahuika
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
Available Modules
RAxML-NG
Mahuika
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
Available Modules
Links
RDP-Classifier
Mahuika
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
Links
RE2
Mahuika
fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++library.
Available Modules
Links
RECON
Biology
Mahuika
De novo identification and classification of repeat sequence families from genomic sequences
Available Modules
Links
REViewer
Mahuika
Tool for visualizing alignments of reads in regions containing tandem repeats
Available Modules
Links
RFPlasmid
Mahuika
Predicting plasmid contigs from assemblies
Available Modules
Links
RFdiffusion
Mahuika
Structure generation, with or without conditional information (a motif, target etc) It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.
Available Modules
Links
RMBlast
Biology
Mahuika
RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include: Support for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-like masklevel filtering..
Available Modules
Links
RNAmmer
Mahuika
consistent and rapid annotation of ribosomal RNA genes.
Available Modules
Links
ROCm
Mahuika
Platform for GPU Enabled HPC and UltraScale Computing
Available Modules
Links
ROOT
Mahuika
The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.
Available Modules
Links
RSEM
Biology
Mahuika
Estimates gene and isoform expression levels from RNA-Seq data
Available Modules
Links
RSGISLib
Earth_science
Mahuika
The Remote Sensing and GIS software library (RSGISLib) is a collection of tools for processing remote sensing and GIS datasets. The tools are accessed using Python bindings or an XML interface.
Available Modules
module load RSGISLib/5.0.10-gimkl-2022a-Python-3.10.5
Links
Racon
Mahuika
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
Available Modules
module load Racon/1.5.0-GCC-11.3.0
Links
Ragout
Mahuika
Tool for chromosome assembly using multiple references.
Available Modules
Links
RapidNJ
Mahuika
An algorithmic engineered implementation of canonical neighbour-joining.
Available Modules
Links
Raven
Mahuika
De novo genome assembler for long uncorrected reads.
Available Modules
Links
Rcorrector
Mahuika
kmer-based error correction method for RNA-seq data.
Available Modules
Links
Relion
Biology
No_toc
No_lic
No_desc
No_ver
Mahuika
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
Available Modules
RepeatMasker
Biology
Mahuika
Screens DNA sequences for interspersed repeats and low complexity DNA sequences. For licensing reasons RepBase is not included, instead you must set LIBDIR to point at a directory which contains your copy of it.
Available Modules
module load RepeatMasker/4.1.0-gimkl-2020a
Links
RepeatModeler
Mahuika
De novo transposable element (TE) family identification and modeling package.
Available Modules
Links
RepeatScout
Biology
Mahuika
De novo identification of repeat families in large genomes
Available Modules
Links
Riskscape
Mahuika
RiskScape is an open-source spatial data processing application used for multi-hazard risk analysis. RiskScape is highly customisable, letting modellers tailor the risk analysis to suit the problem domain and input data being modelled.
Available Modules
Links
Roary
Mahuika
Rapid large-scale prokaryote pan genome analysis
Available Modules
Links
Rosetta
Mahuika
Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.
Available Modules
Links
Rstudio
Language
Maui_ancil
RStudio is a set of integrated tools designed to help you be more productive with R.
Available Modules
Links
Ruby
Language
Mahuika
Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Available Modules
Links
Rust
Mahuika
Systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
Available Modules
module load Rust/1.76.0-GCC-12.3.0
Links
SAGE
Mahuika
Ppackage containing programs for use in the genetic analysis of family, pedigree and individual data.
Available Modules
Links
SAMtools
Biology
Mahuika
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
Available Modules
module load SAMtools/1.19-GCC-12.3.0
Links
SAS
Mahuika
Maui
SAS is a statistical software suite developed by SAS Institute for data management, advanced analytics, multivariate analysis, business intelligence, criminal investigation, and predictive analytics. - Homepage: https://www.sas.com/en_nz/home.html/
SCOTCH
Mathematics
Mahuika
Maui
Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
Available Modules
module load SCOTCH/7.0.4-foss-2023a
module load SCOTCH/6.0.4-CrayIntel-23.02-19
Links
SCons
Mahuika
Maui
SCons is a software construction tool.
Links
SDL2
Mahuika
Simple DirectMedia Layer, a cross-platform multimedia library
Available Modules
Links
SEPP
Mahuika
SATe-enabled Phylogenetic Placement. Phylogenetic placement of short reads into reference alignments and trees.
Available Modules
module load SEPP/4.5.1-gimkl-2022a-Python-3.11.3
Links
SHAPEIT4
Mahuika
Estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.
Available Modules
Links
SIONlib
Mahuika
Scalable I/O library for parallel access to task-local files.
Available Modules
Links
SIP
Mahuika
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
Available Modules
module load SIP/4.19.15-gimkl-2020a-Python-3.8.2
Links
SKESA
Mahuika
SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.
Available Modules
Links
SMRT-Link
Mahuika
PacBio’s open-source software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
Available Modules
module load SMRT-Link/11.1.0.166339-cli-tools-only
Links
SNVoter-NanoMethPhase
Mahuika
SNVoter - A top up tool to enhance SNV calling from Nanopore sequencing data & NanoMethPhase - Phase long reads and CpG methylations from Oxford Nanopore Technologies.
Available Modules
SOCI
Mahuika
Database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
Available Modules
Links
SPAdes
Biology
Mahuika
Genome assembler for single-cell and isolates data sets
Available Modules
module load SPAdes/3.15.4-gimkl-2022a-Python-3.10.5
Links
SPECFEM3D
Earth_science
Maui
SPECFEM3D Cartesian simulates acoustic (fluid), elastic (solid), coupled acoustic/elastic, poroelastic or seismic wave propagation in any type of conforming mesh of hexahedra (structured or not.) It can, for instance, model seismic waves propagating in sedimentary basins or any other regional geological model following earthquakes. It can also be used for non-destructive testing or for ocean acoustics.
Available Modules
Links
SPIDER
Mahuika
System for Processing Image Data from Electron microscopy and Related fields
Available Modules
Links
SQLite
Mahuika
Maui
Maui_ancil
SQLite: SQL Database Engine in a C Library
Available Modules
module load SQLite/3.42.0-GCCcore-12.3.0
module load SQLite/3.36.0-CrayIntel-23.02-19
module load SQLite/3.31.1-GCC-9.2.0
Links
SQLplus
Maui_ancil
SQL*Plus is an interactive and batch query tool that is installed with every Oracle Database installation. It has a command-line user interface and a Windows Graphical User Interface (GUI).
Available Modules
Links
SSAHA2
Mahuika
Pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
Available Modules
Links
STAR
Biology
Mahuika
Fast universal RNA-seq aligner
Available Modules
module load STAR/2.7.10b-GCC-11.3.0-alpha
Links
STAR-Fusion
Mahuika
Processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set
Available Modules
Links
SUNDIALS
Mathematics
Mahuika
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
Available Modules
module load SUNDIALS/5.8.0-gimkl-2020a
Links
SURVIVOR
Mahuika
Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
Links
SWIG
Mahuika
Maui_ancil
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
Links
Salmon
Biology
Mahuika
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
Available Modules
module load Salmon/1.9.0-GCC-11.3.0
Links
Sambamba
Biology
Mahuika
Tools for working with SAM/BAM data
Links
ScaLAPACK
Mahuika
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
Available Modules
Links
Scalasca
Mahuika
Tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.
Available Modules
Links
Score-P
Mahuika
Measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
Available Modules
Links
SeisSol
Mahuika
SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG).
Available Modules
Links
SeqAn
Mahuika
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
Available Modules
Links
SeqAn3
Mahuika
C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
Links
SeqKit
Mahuika
Ultrafast toolkit for FASTA/Q file manipulation
Links
SiBELia
Mahuika
A comparative genomics tool for analysing genomic variations that correlate with pathogens, or microorganisms adapt in different environments.
Available Modules
Links
Siesta
Physics
Mahuika
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
Available Modules
module load Siesta/5.0.0-foss-2023a
Links
SignalP
Mahuika
SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
Available Modules
Links
Singularity
Containers
Singularity
Docker
Mahuika
Maui_ancil
Sniffles
Mahuika
A fast structural variant caller for long-read sequencing.
Available Modules
module load Sniffles/2.3.3-gimkl-2022a-Python-3.10.5
Links
SortMeRNA
Biology
Mahuika
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
Available Modules
Links
SourceTracker
Biology
Mahuika
SourceTracker is a Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments.
Available Modules
Links
Spack
Mahuika
Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
Links
Spark
Mahuika
Maui_ancil
Spark is Hadoop MapReduce done in memory
Available Modules
module load Spark/2.3.1-gimkl-2018b-Hadoop-2.7
module load Spark/2.3.1-gimkl-2018b-Hadoop-2.7
Links
SqueezeMeta
Mahuika
fully automated metagenomics pipeline, from reads to bins.
Available Modules
Links
Stacks
Biology
Mahuika
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Available Modules
module load Stacks/2.65-GCC-11.3.0
Links
StringTie
Mahuika
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
Available Modules
module load StringTie/2.2.0-gimkl-2022a
Links
Structure
Mahuika
The program structure is a free software package for using multi-locus genotype data to investigate population structure.
Available Modules
Links
Subread
Biology
Mahuika
High performance read alignment, quantification and mutation discovery
Available Modules
Links
Subversion
Mahuika
Maui_ancil
Subversion is an open source version control system.
Available Modules
module load Subversion/1.9.7
module load Subversion/1.13.0-GCC-9.2.0
Links
SuiteSparse
Mahuika
SuiteSparse is a collection of libraries manipulate sparse matrices.
Available Modules
Links
SuperLU
Mahuika
Solution of large, sparse, nonsymmetric systems of linear equations.
Available Modules
Links
Supernova
Biology
Mahuika
Mahuika
Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source
Available Modules
Szip
Mahuika
Maui_ancil
Szip compression software, providing lossless compression of scientific data
Available Modules
module load Szip/2.1.1-GCCcore-12.3.0
module load Szip/2.1.1-iccifort-2020.0.166
Links
TEtranscripts
Mahuika
Takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.
Available Modules
Links
TMHMM
Mahuika
Prediction of transmembrane helices in proteins
Available Modules
Links
TOGA
Mahuika
Implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes.
Available Modules
Links
TSEBRA
Mahuika
Transcript Selector for BRAKER
Available Modules
module load TSEBRA/1.1.1-gimkl-2022a-Python-3.11.3
Links
TURBOMOLE
Mahuika
Program Package For Electronic Structure Calculations.
Available Modules
Links
TWL-NINJA
Mahuika
Nearly Infinite Neighbor Joining Application.
Available Modules
Links
Tcl
Language
Mahuika
Maui
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
Available Modules
module load Tcl/8.6.10-GCCcore-12.3.0
module load Tcl/8.6.7-CrayIntel-23.02-19
Links
TensorFlow
Machine_learning
Mahuika
An open-source software library for Machine Intelligence
Available Modules
module load TensorFlow/2.13.0-gimkl-2022a-Python-3.11.3
Links
TensorRT
Mahuika
NVIDIA TensorRT is a platform for high-performance deep learning inference
Available Modules
module load TensorRT/8.6.1.6-gimkl-2022a-Python-3.11.3-CUDA-11.8.0
Links
Theano
Mahuika
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
Available Modules
Links
Tk
Mahuika
Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
Available Modules
module load Tk/8.6.10-GCCcore-12.3.0
Links
TransDecoder
Mahuika
TransDecoder identifies candidate coding regions within transcript sequences.
Available Modules
module load TransDecoder/5.7.1-GCC-11.3.0-Perl-5.34.1
Links
Transrate
Mahuika
Available Modules
Links
TreeMix
Mahuika
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
Available Modules
Links
TrimGalore
Biology
Mahuika
A wrapper of FastQC and cutadapt to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files
Available Modules
module load TrimGalore/0.6.10-gimkl-2022a-Python-3.11.3-Perl-5.34.1
Links
Trimmomatic
Mahuika
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Available Modules
Links
Trinity
Biology
Mahuika
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
Available Modules
module load Trinity/2.14.0-gimkl-2022a
Trinotate
Mahuika
C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
Available Modules
Links
Trycycler
Mahuika
Tool for generating consensus long-read assemblies for bacterial genomes.
Available Modules
module load Trycycler/0.5.4-gimkl-2022a-Python-3.10.5
Links
TuiView
Earth_science
Mahuika
TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.
Available Modules
module load TuiView/1.2.10-gimkl-2020a-Python-3.8.2
Links
TurboVNC
Mahuika
TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.
Available Modules
UCC
Mahuika
UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.
Available Modules
Links
UCX
Mahuika
Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
Available Modules
module load UCX/1.14.1-GCCcore-12.3.0
Links
UDUNITS
Physics
Mahuika
Maui
Maui_ancil
UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
Available Modules
module load UDUNITS/2.2.28-GCCcore-12.3.0
module load UDUNITS/2.2.28-CrayGNU-23.02
module load UDUNITS/2.2.25-GCC-7.1.0
Links
USEARCH
Mahuika
USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
Available Modules
Links
Unicycler
Mahuika
Assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser.
Available Modules
module load Unicycler/0.5.0-gimkl-2020a-Python-3.8.2
Links
VASP
Chemistry
Mahuika
Density functional theory
Molecular dynamics
Computational chemistry
Mahuika
Maui
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
Available Modules
module load VASP/6.4.2-intel-2022a
module load VASP/6.3.2-CrayIntel-23.02-19
Licence
VASP is proprietary software.
VCF-kit
Mahuika
VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.
Available Modules
Links
VCFtools
Biology
Mahuika
The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.
Available Modules
module load VCFtools/0.1.15-GCC-9.2.0-Perl-5.30.1
Links
VEP
Mahuika
Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.
Available Modules
module load VEP/107.0-GCC-11.3.0-Perl-5.34.1
Links
VESTA
Maui_ancil
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Run 'VESTA-gui' to launch.
Available Modules
Links
VIBRANT
Mahuika
Virus Identification By iteRative ANnoTation
Available Modules
Links
VMD
Mahuika
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Available Modules
Links
VSEARCH
Biology
Mahuika
An open source alternative to the metagenomics tool USEARCH. Performs chimera detection, clustering, full-length and prefix dereplication, rereplication, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
Available Modules
module load VSEARCH/2.21.1-GCC-11.3.0
Links
VTK
Visualisation
Mahuika
Maui_ancil
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
Available Modules
module load VTK/7.1.1-gimkl-2018b-Python-2.7.16
module load VTK/8.1.1-GCC-7.1.0-Anaconda2-5.2.0
Links
VTune
Mahuika
Maui_ancil
Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
Available Modules
Valgrind
Mahuika
Maui_ancil
Valgrind: Debugging and profiling tools
Available Modules
module load Valgrind/3.19.0-GCC-11.3.0
module load Valgrind/3.14.0-GCC-7.1.0
Links
VarScan
Mahuika
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
Available Modules
Links
Velvet
Biology
Mahuika
Sequence assembler for very short reads
Available Modules
Links
VelvetOptimiser
Mahuika
Perl script for optimising the three primary parameter options of the Velvet de novo sequence assembler.
Available Modules
Links
ViennaRNA
Biology
Mahuika
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
Available Modules
Links
Vim
Mahuika
Maui_ancil
Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set.
Links
VirHostMatcher
Mahuika
Tools for computing various oligonucleotide frequency (ONF) based distance/dissimialrity measures.
Available Modules
Links
VirSorter
Mahuika
VirSorter: mining viral signal from microbial genomic data.
Available Modules
module load VirSorter/2.2.3-gimkl-2020a-Python-3.8.2
VirtualGL
Mahuika
VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.
Available Modules
Links
VisIt
Visualisation
Maui_ancil
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. This version supports interactive CPU-only rendering with the VisIt GUI using the Mesa library. It does not support GPU rendering. Use the GALLIUM_DRIVER environment variable to choose a software renderer, it is recommended to use GALLIUM_DRIVER=swr for best performance.
Available Modules
Links
WAAFLE
Mahuika
Workflow to Annotate Assemblies and Find LGT Events.
Available Modules
Links
WhatsHap
Mahuika
Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.
Available Modules
Links
Winnowmap
Mahuika
Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.
Available Modules
Links
Wise2
Biology
Mahuika
Aligning proteins or protein HMMs to DNA
Available Modules
Links
XCONV
Visualisation
Maui_ancil
Xconv is a program designed to convert model output into a format suitable for use in various plotting packages. Xconv is designed to be simple to use with a point and click, windows based interface.
Available Modules
Links
XHMM
Mahuika
Calls copy number variation (CNV) from normalized read-depth data from exome capture or other targeted sequencing experiments.
Available Modules
Links
XIOS
Maui
XIOS stands for XML-IO-Server and is a library dedicated to I/O management in climate codes. This version uses netCDF4 with the parallel HDF5 library, and it contains a patch for various problems in the mesh connectivity algorithm
Available Modules
module load XIOS/r2279-CrayIntel-23.02-19-NC4PAR-patched
Links
XMDS2
Mahuika
Fast integrator of stochastic partial differential equations.
Available Modules
Links
XSD
Mahuika
CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. Provided with an XML instance specification (XML Schema), it generates C++ classes that represent the given vocabulary as well as XML parsing and serialization code. You can then access the data stored in XML using types and functions that semantically correspond to your application domain rather than dealing with the intricacies of reading and writing XML
Available Modules
Links
XZ
Mahuika
Maui
Maui_ancil
xz: XZ utilities
Available Modules
module load XZ/5.4.2-GCCcore-12.3.0
module load XZ/5.4.1-CrayIntel-23.02-19
module load XZ/5.2.5-GCCcore-9.2.0
Links
Xerces-C++
Mahuika
Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
Available Modules
module load Xerces-C++/3.2.3-GCCcore-9.2.0
Links
YAXT
Mahuika
Maui
Yet Another eXchange Tool - Library that performs halo exchange with MPI for domain decomposed simulations.
Available Modules
module load YAXT/0.9.3.1-gimpi-2022a
module load YAXT/0.9.0-CrayGNU-23.02
Links
Yasm
Language
Mahuika
Maui_ancil
Yasm: Complete rewrite of the NASM assembler with BSD license
Available Modules
module load Yasm/1.3.0-gimkl-2017a
module load Yasm/1.3.0-GCC-7.1.0
Links
Z3
Mahuika
A theorem prover from Microsoft Research.
Available Modules
Links
ZeroMQ
Mahuika
ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply.
Available Modules
module load ZeroMQ/4.3.5-GCCcore-12.3.0
Links
Zip
Mahuika
Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
Available Modules
Links
abritamr
Mahuika
AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates
Available Modules
Links
angsd
Biology
Mahuika
Program for analysing NGS data.
Available Modules
Links
ant
Mahuika
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
Available Modules
Links
antiSMASH
Mahuika
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
Available Modules
module load antiSMASH/6.0.1-gimkl-2020a-Python-3.8.2
Links
any2fasta
Mahuika
Convert various sequence formats to FASTA
Available Modules
Links
argtable
Mahuika
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
Available Modules
Links
aria2
Mahuika
aria2 is a lightweight multi-protocol & multi-source command-line download utility.
Available Modules
Links
arpack-ng
Mahuika
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
Available Modules
module load arpack-ng/3.8.0-intel-2022a
Links
at-spi2-atk
Mahuika
AT-SPI 2 toolkit bridge
Available Modules
Links
at-spi2-core
Mahuika
Assistive Technology Service Provider Interface.
Available Modules
Links
attr
Mahuika
Commands for Manipulating Filesystem Extended Attributes
Available Modules
Links
azul-zulu
Mahuika
Java Development Kit (JDK), and a compliant implementation of the Java Standard Edition (SE) specification.
Available Modules
Links
bamUtil
Mahuika
Repository that contains several programs that perform operations on SAM/BAM files.
Available Modules
Links
barrnap
Mahuika
Barrnap predicts the location of ribosomal RNA genes in genomes.
Available Modules
Links
bcl2fastq2
Biology
Mahuika
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
Available Modules
Links
beagle-lib
Mahuika
Available Modules
module load beagle-lib/20170904-gimkl-2017a
Links
best
Mahuika
Bam Error Stats Tool (best): analysis of error types in aligned reads
Available Modules
Links
binutils
Mahuika
Maui_ancil
binutils: GNU binary utilities
Available Modules
module load binutils/2.40
module load binutils/2.32
Links
bioawk
Mahuika
An extension to awk, adding the support of several common biological data formats
Available Modules
Links
breseq
Mahuika
breseq is a computational pipeline for the analysis of short-read re-sequencing data
Available Modules
module load breseq/0.38.3-gimkl-2022a-R-4.3.1
Links
bsddb3
Mahuika
bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.
Available Modules
Links
bzip2
Mahuika
Maui_ancil
bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
Available Modules
module load bzip2/1.0.8-GCCcore-12.3.0
module load bzip2/1.0.8-GCCcore-9.2.0
Links
c-ares
Mahuika
c-ares is a C library for asynchronous DNS requests (including name resolves)
Available Modules
Links
cURL
Mahuika
Maui_ancil
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
Available Modules
module load cURL/8.3.0-GCCcore-12.3.0
module load cURL/7.83.1-GCCcore-9.2.0
Links
cairo
Mahuika
Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
Available Modules
module load cairo/1.17.8-GCC-12.3.0
Links
cdbfasta
Mahuika
Fasta file indexing and retrival tool
Available Modules
Links
cdt
Maui
Available Modules
Links
chewBBACA
Mahuika
A complete suite for gene-by-gene schema creation and strain identification..
Available Modules
Links
chopper
Mahuika
Rust implementation of NanoFilt+NanoLyse
Available Modules
Links
compleasm
Mahuika
faster and more accurate reimplementation of BUSCO.
Available Modules
Links
cromwell
Workflow_management
Mahuika
Workflow Management System geared towards scientific workflows.
Available Modules
Links
ctags
Mahuika
Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.
Available Modules
Links
ctffind
Biology
Mahuika
ctffind is a program for finding CTFs of electron micrographs
Available Modules
Links
cuDNN
Mahuika
Maui_ancil
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
Available Modules
module load cuDNN/8.9.7.29-CUDA-12.2.2
module load cuDNN/8.6.0.163-CUDA-11.8.0
Links
cutadapt
Biology
Mahuika
cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
Available Modules
module load cutadapt/4.4-gimkl-2022a-Python-3.11.3
Links
cuteSV
Mahuika
Fast and scalable long-read-based SV detection
Available Modules
Links
cwltool
Mahuika
Common Workflow Language tool description reference implementation
Available Modules
module load cwltool/3.0.20200317203547-gimkl-2020a-Python-3.8.2
Links
cyvcf2
Mahuika
cython + htslib == fast VCF and BCF processing
Available Modules
Links
dadi
Mahuika
Diffusion Approximation for Demographic Inference
Available Modules
Links
dammit
Mahuika
de novo transcriptome annotator..
Available Modules
Links
datasets
Mahuika
Tool to gather data from across NCBI databases
Available Modules
Links
deepTools
Mahuika
deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
Available Modules
Links
devtools
Mahuika
R functions that simplify and expedite common tasks in package development.
Available Modules
Links
double-conversion
Mahuika
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
Available Modules
module load double-conversion/3.2.1-GCC-11.3.0
drep
Mahuika
Rapid and accurate comparison and de-replication of microbial genomes
Available Modules
module load drep/3.4.2-gimkl-2022a-Python-3.10.5
Links
dtcmp
Mahuika
DTCMP Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes.
Available Modules
Links
duphold
Mahuika
uphold your DUP and DEL calls
Available Modules
Links
duplex-tools
Mahuika
Range of tools to support operations on Duplex Sequencing read pairs.
Available Modules
Links
eDNA
Mahuika
A suite of tools to conduct metabarcoding analyses targeting any group of organisms. Includes utilities for preprocessing raw data and building your own custom reference database.
Available Modules
Links
easi
Mahuika
easi is a library for the Easy Initialization of models in three (or less or more) dimensional domains.
Available Modules
Links
ecCodes
Mahuika
ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
Available Modules
module load ecCodes/2.30.0-gimpi-2022a
Links
eccodes
Maui
Maui_ancil
ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: - WMO FM-92 GRIB edition 1 and edition 2 - WMO FM-94 BUFR edition 3 and edition 4 - WMO GTS abbreviated header (only decoding) A useful set of command line tools provide quick access to the messages.
Available Modules
module load eccodes/2.8.0-CrayIntel-23.02-19
module load eccodes/2.16.0-GCC-7.1.0
Links
ectyper
Mahuika
Standalone versatile serotyping module for Escherichia coli..
Available Modules
Links
edlib
Mahuika
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
Available Modules
Links
eggnog-mapper
Mahuika
Tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments
Available Modules
Links
emmtyper
Mahuika
Tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly
Available Modules
Links
ensmallen
Mahuika
C++ header-only library for numerical optimization
Available Modules
Links
entrez-direct
Mahuika
an advanced method for accessing the NCBI's set of interconnected databases such as publication, sequence, structure, gene, variation, expression, etc.
Available Modules
Links
exonerate
Biology
Mahuika
Generic tool for pairwise sequence comparison
Available Modules
module load exonerate/2.4.0-GCC-11.3.0
Links
expat
Mahuika
Maui
Maui_ancil
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
Available Modules
module load expat/2.5.0-GCCcore-12.3.0
module load expat/2.4.1-CrayIntel-23.02-19
module load expat/2.4.1-GCCcore-9.2.0
Links
fastStructure
Biology
Mahuika
fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
Available Modules
Links
fastp
Mahuika
A tool designed to provide fast all-in-one preprocessing for FastQ files.
Available Modules
Links
fastq-tools
Mahuika
A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.
Available Modules
Links
fcGENE
Mahuika
Format converting tool for genotype Data.
Available Modules
Links
fgbio
Mahuika
A set of tools to analyze genomic data with a focus on Next Generation Sequencing.
Available Modules
Links
fineRADstructure
Mahuika
A package for population structure inference from RAD-seq data
Available Modules
fineSTRUCTURE
Mahuika
Population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence dat
Available Modules
Links
flatbuffers
Mahuika
FlatBuffers: Memory Efficient Serialization Library
Available Modules
Links
fmlrc
Mahuika
Tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data
Available Modules
Links
fmt
Mahuika
Formatting library providing a fast and safe alternative to C stdio and C++ iostreams.
Available Modules
Links
fontconfig
Mahuika
Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
Available Modules
module load fontconfig/2.14.2-GCCcore-12.3.0
Links
forge
Mahuika
Maui
Maui_ancil
Arm Forge combines Arm DDT, the leading debugger for time-saving high performance application debugging, and Arm MAP, the trusted performance profiler for invaluable optimization advice.
foss
Mahuika
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
Links
freetype
Mahuika
FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
Available Modules
module load freetype/2.13.2-GCCcore-12.3.0
Links
funcx-endpoint
Mahuika
funcX is a distributed Function as a Service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. Unlike centralized FaaS platforms, funcX allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A funcX endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.
Available Modules
module load funcx-endpoint/1.0.11-gimkl-2022a-Python-3.10.5
Links
fxtract
Mahuika
Extract sequences from a fastx (fasta or fastq) file given a subsequence.
Available Modules
Links
g2clib
Mahuika
Library contains GRIB2 encoder/decoder ('C' version).
Available Modules
Links
g2lib
Mahuika
Library contains GRIB2 encoder/decoder and search/indexing routines.
Available Modules
Links
ga4gh
Mahuika
A reference implementation of the GA4GH API
Available Modules
Links
geany
Mahuika
Maui
A GTK+ based text editor with with basic features of an integrated development environment.
Links
genometools
Mahuika
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations.
Available Modules
Links
gettext
Mahuika
Maui_ancil
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
Available Modules
module load gettext/0.21
module load gettext/0.21
Links
gfastats
Mahuika
single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
Available Modules
Links
gffread
Mahuika
GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
Available Modules
Links
giflib
Mahuika
giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
Available Modules
Links
gimkl
Mahuika
Maui_ancil
gimpi
Mahuika
Maui_ancil
git
Mahuika
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
Available Modules
Links
globus-automate-client
Mahuika
Client for the Globus Flows service.
Available Modules
globus-compute-endpoint
Mahuika
Globus Compute is a distributed Function as a Service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. Unlike centralized FaaS platforms, Globus Compute allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A Globus Compute endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.
Available Modules
module load globus-compute-endpoint/2.19.0-gimkl-2022a-Python-3.10.5
gmsh
Mahuika
Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor..
Available Modules
Links
gnuplot
Mahuika
Maui_ancil
Portable interactive, function plotting utility
Available Modules
module load gnuplot/5.4.2-GCC-7.4.0
module load gnuplot/5.4.2-GCC-7.1.0
Links
gompi
Mahuika
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
Links
google-sparsehash
Mahuika
An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.
Available Modules
googletest
Mahuika
Google's C++ test framework
Available Modules
Links
gperf
Mahuika
Pperfect hash function generator.
Available Modules
Links
grib_api
Maui
Maui_ancil
The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages. Note that JPEG and Python support have been disabled for this build.
Available Modules
module load grib_api/1.23.1-CrayIntel-23.02-19
module load grib_api/1.23.1-iccifort-2018.1.163-GCC-7.1.0
Links
grive2
Mahuika
Command line tool for Google Drive.
Available Modules
Links
gsort
Mahuika
Tool to sort genomic files according to a genomefile.
Available Modules
Links
h5pp
Mahuika
A simple C++17 wrapper for HDF5.
Available Modules
Links
haplocheck
Mahuika
Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content
Available Modules
Links
help2man
Mahuika
help2man produces simple manual pages from the '--help' and '--version' output of other commands.
Available Modules
Links
hifiasm
Mahuika
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.
Available Modules
Links
hunspell
Mahuika
Spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.
Available Modules
Links
hwloc
Mahuika
The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
Available Modules
Links
hypothesis
Mahuika
Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
Available Modules
Links
icc
Mahuika
Maui_ancil
Intel C and C++ compilers
Available Modules
module load icc/2018.1.163-GCC-7.4.0
module load icc/2018.1.163-GCC-7.1.0
Links
iccifort
Mahuika
Maui_ancil
Intel C, C++ & Fortran compilers
Available Modules
module load iccifort/2020.0.166
module load iccifort/2020.0.166
Links
ifort
Mahuika
Maui_ancil
Intel Fortran compiler
Available Modules
module load ifort/2018.1.163-GCC-7.4.0
module load ifort/2018.1.163-GCC-7.1.0
Links
iimpi
Mahuika
Maui_ancil
imkl
Mathematics
Mahuika
Maui_ancil
Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
Available Modules
module load imkl/2022.0.2
module load imkl/2020.0.166-iimpi-2020a
Links
imkl-FFTW
Mahuika
FFTW interfaces using Intel oneAPI Math Kernel Library
Available Modules
Links
impalajit
Mahuika
A lightweight JIT compiler for flexible data access in simulation applications
Available Modules
Links
impi
Mahuika
Maui_ancil
Intel MPI Library, compatible with MPICH ABI
Available Modules
module load impi/2021.5.1-intel-compilers-2022.0.2
module load impi/2019.6.166-iccifort-2020.0.166
Links
intel
Mahuika
Maui_ancil
intel-compilers
Mahuika
Intel C, C++ & Fortran compilers (classic and oneAPI)
Available Modules
Links
ipyrad
Mahuika
ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.
Available Modules
module load ipyrad/0.9.85-gimkl-2022a-Python-3.10.5
ispc
Mahuika
Maui_ancil
Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.
Available Modules
module load ispc/1.15.0
module load ispc/1.9.2-GCC-7.1.0
Links
jbigkit
Mahuika
JBIG-KIT is a software implementation of the JBIG1 data compression standard
Available Modules
Links
jcvi
Mahuika
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Available Modules
Links
jemalloc
Mahuika
A general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
Available Modules
module load jemalloc/5.3.0
Links
jq
Mahuika
Lightweight and flexible command-line JSON processor.
Available Modules
Links
json-c
Mahuika
JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
Available Modules
Links
jvarkit
Mahuika
Java utilities for Bioinformatics
Available Modules
Links
kalign2
Mahuika
Kalign is a fast multiple sequence alignment program for biological sequences.
Available Modules
Links
kallisto
Biology
Mahuika
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Available Modules
Links
kineto
Mahuika
A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters
Available Modules
Links
kma
Mahuika
KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
Available Modules
Links
libFLAME
Mahuika
libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.
Available Modules
Links
libGLU
Mahuika
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
Available Modules
Links
libKML
Mahuika
Maui_ancil
Reference implementation of OGC KML 2.2
Available Modules
module load libKML/1.3.0.2017-GCC-12.3.0
module load libKML/1.3.0.2017-GCC-9.2.0
Links
libStatGen
Mahuika
Set of classes for creating statistical genetic programs.
Available Modules
Links
libarchive
Mahuika
Multi-format archive and compression library
Available Modules
Links
libcircle
Mahuika
API for distributing embarrassingly parallel workloads using self-stabilization.
Available Modules
Links
libdeflate
Mahuika
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
Available Modules
Links
libdrm
Mahuika
Direct Rendering Manager runtime library.
Available Modules
Links
libdwarf
Mahuika
The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers
Available Modules
Links
libepoxy
Mahuika
Library for handling OpenGL function pointer management
Available Modules
Links
libevent
Mahuika
Maui_ancil
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
Links
libffi
Mahuika
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
Available Modules
module load libffi/3.4.2
Links
libgcrypt
Mahuika
Libgpg-error is a small library that defines common error values for all GnuPG components.
Available Modules
Links
libgd
Mahuika
Maui_ancil
GD is an open source code library for the dynamic creation of images by programmers.
Available Modules
module load libgd/2.3.3-GCCcore-12.3.0
module load libgd/2.2.5-GCC-7.1.0
Links
libgeotiff
Mahuika
Maui_ancil
Library for reading and writing coordinate system information from/to GeoTIFF files
Available Modules
module load libgeotiff/1.7.1-GCCcore-11.3.0
module load libgeotiff/1.7.1-GCC-9.2.0-PROJ-9.1.1
Links
libgit2
Mahuika
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.
Available Modules
Links
libglvnd
Mahuika
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
Available Modules
Links
libgpg-error
Mahuika
Libgpg-error is a small library that defines common error values for all GnuPG components.
Available Modules
Links
libgpuarray
Mathematics
Mahuika
Arrays on GPU device memory, for Theano
Available Modules
Links
libgtextutils
Mahuika
ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
Available Modules
Links
libiconv
Mahuika
Maui_ancil
Libiconv converts from one character encoding to another through Unicode conversion
Available Modules
module load libiconv/1.17-GCC-12.3.0
module load libiconv/1.15-GCC-7.1.0
Links
libjpeg-turbo
Mahuika
Maui
Maui_ancil
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
Available Modules
module load libjpeg-turbo/2.1.5.1-GCCcore-12.3.0
module load libjpeg-turbo/2.0.2-CrayGNU-23.02
module load libjpeg-turbo/2.1.3-GCCcore-9.2.0
Links
libmatheval
Mathematics
Mahuika
GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
Available Modules
Links
libpciaccess
Mahuika
Generic PCI access library.
Available Modules
Links
libpng
Mahuika
Maui
Maui_ancil
libpng is the official PNG reference library
Available Modules
module load libpng/1.6.40-GCCcore-12.3.0
module load libpng/1.6.37-CrayGNU-23.02
module load libpng/1.6.37-GCCcore-9.2.0
Links
libreadline
Mahuika
Maui
Maui_ancil
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Available Modules
module load libreadline/8.2-GCCcore-12.3.0
module load libreadline/8.1-CrayIntel-23.02-19
module load libreadline/8.0-GCCcore-7.1.0
Links
libspatialite
Mahuika
SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
Available Modules
module load libspatialite/5.0.1-GCCcore-11.3.0
Links
libtool
Mahuika
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
Available Modules
Links
libunistring
Mahuika
This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
Available Modules
Links
libunwind
Mahuika
Define a portable and efficient C programming API to determine the call-chain of a program.
Available Modules
Links
libvdwxc
Mahuika
libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.
Available Modules
Links
libvpx
Maui_ancil
The WebM Project is dedicated to developing a high-quality, open video format for the web that's freely available to everyone.
Available Modules
Links
libxc
Chemistry
Mahuika
Maui
Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
Available Modules
module load libxc/6.2.2-intel-2022a
module load libxc/4.2.3-CrayGNU-23.02
Links
libxml2
Mahuika
Maui
Maui_ancil
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
Available Modules
module load libxml2/2.11.4-GCCcore-12.3.0
module load libxml2/2.9.9-CrayIntel-23.02-19
module load libxml2/2.9.10-GCCcore-9.2.0
Links
libxslt
Mahuika
Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
Available Modules
module load libxslt/1.1.38-GCCcore-12.3.0
Links
libxsmm
Mathematics
Mahuika
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
Available Modules
module load libxsmm/1.17-GCC-12.3.0
Links
libzstd
Mahuika
Fast lossless compression algorithm.
Available Modules
Links
lighttpd
Mahuika
A web server.
Available Modules
Links
likwid
Mahuika
Command line tools for Linux to support programmers in developing high performance multi threaded programs.
Available Modules
Links
lp_solve
Mathematics
Mahuika
Mixed Integer Linear Programming (MILP) solver
Available Modules
module load lp_solve/5.5.2.11-GCC-11.3.0
Links
lwgrp
Mahuika
The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set.
Available Modules
Links
lz4
Mahuika
Maui_ancil
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
Available Modules
module load lz4/1.9.4-GCCcore-12.3.0
module load lz4/1.9.3-GCCcore-9.2.0
Links
maf_stream
Mahuika
Collection of utilities to manipulate multiple alignments in the Multiple Alignment Format
Available Modules
Links
magma
Mahuika
The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
Available Modules
module load magma/2.7.1-gimkl-2022a-CUDA-11.6.2
Links
makedepend
Maui_ancil
The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
Available Modules
Links
manta
Mahuika
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
Available Modules
Links
mapDamage
Mahuika
tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
Available Modules
Links
meRanTK
Mahuika
High performance toolkit for complete analysis of methylated RNA data.
Available Modules
Links
medaka
Mahuika
Medaka is a tool to create a consensus sequence from nanopore sequencing data.
Available Modules
module load medaka/1.11.1-Miniconda3-22.11.1-1
Links
megalodon
Mahuika
Tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transcriptome.
Available Modules
module load megalodon/2.5.0-gimkl-2022a-Python-3.10.5
Links
metaWRAP
Mahuika
Flexible pipeline for genome-resolved metagenomic data analysis.
Available Modules
Links
miRDeep2
Mahuika
Completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
Available Modules
Links
midl
Maui_ancil
The Met Office library is a collection of routines written in IDL at the Met Office, originally written in PV-WAVE in the Hadley Centre in the early 1990s, with development continuing to the present day. Its main purpose is to support analysis and visualisation of PP data produced by the Unified Model (UM).
Available Modules
Links
mimalloc
Mahuika
mimalloc is a general purpose allocator with excellent performance characteristics.
Available Modules
Links
miniBUSCO
Mahuika
faster and more accurate reimplementation of BUSCO.
Available Modules
Links
miniasm
Mahuika
Fast OLC-based de novo assembler for noisy long reads.
Available Modules
Links
minimap2
Mahuika
Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. .
Available Modules
module load minimap2/2.28-GCC-12.3.0
Links
miniprot
Mahuika
Aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift..
Available Modules
Links
mjpegtools
Maui_ancil
The mjpeg programs are a set of tools that can do recording of videos and playback, simple cut-and-paste editing and the MPEG compression of audio and video under Linux.
Available Modules
Links
mlpack
Mahuika
Fast, and flexible C++ machine learning library with bindings to other languages
Available Modules
Links
mo_tidl
Maui_ancil
The Met Office library is a collection of routines written in IDL at the Met Office, originally written in PV-WAVE in the Hadley Centre in the early 1990s, with development continuing to the present day. Its main purpose is to support analysis and visualisation of PP data produced by the Unified Model (UM).
Available Modules
module load mo_tidl/20130812-IDL-8.7-GCC-7.1.0
Links
modbam2bed
Mahuika
A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.
Available Modules
Links
modkit
Mahuika
Tool for working with modified bases from Oxford Nanopore
Available Modules
Links
mosdepth
Mahuika
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Available Modules
Links
mpi4py
Maui_ancil
This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/2/3 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.
Available Modules
module load mpi4py/3.0.0-gimpi-2018b-Anaconda3-5.2.0
Links
mpifileutils
Mahuika
MPI-Based File Utilities For Distributed Systems
Available Modules
Links
muParser
Mathematics
Mahuika
muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.
Available Modules
module load muParser/2.2.5-gimkl-2020a
Links
nano
Mahuika
Maui
nano is a text editor.
Links
nanoQC
Mahuika
Create fastQC-like plots for Oxford Nanopore sequencing data.
Available Modules
module load nanoQC/0.9.4-gimkl-2022a-Python-3.10.5
Links
nanofilt
Mahuika
Filtering and trimming of long read sequencing data.
Available Modules
Links
nanoget
Mahuika
Functions to extract information from Oxford Nanopore sequencing data and alignments
Available Modules
module load nanoget/1.18.1-gimkl-2022a-Python-3.10.5
Links
nanomath
Mahuika
A few simple math function for other Oxford Nanopore processing scripts
Available Modules
module load nanomath/1.2.1-gimkl-2022a-Python-3.10.5
Links
nanopolish
Mahuika
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Available Modules
module load nanopolish/0.13.3-gimkl-2020a-Python-3.9.9
Links
ncbi-vdb
Biology
Mahuika
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Available Modules
Links
nccmp
Maui_ancil
nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment.
Available Modules
Links
ncurses
Mahuika
Maui
Maui_ancil
The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
Available Modules
module load ncurses/6.4-GCCcore-12.3.0
module load ncurses/6.2-CrayIntel-23.02-19
module load ncurses/6.1
Links
ncview
Mahuika
Visual browser for netCDF format files.
Available Modules
Links
ne
Mahuika
ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage.
Available Modules
Links
nearline
Mahuika
Maui
NeSI nearline client provides 'End User' access to NeSI's archive filesystem Nearline which is connected to a Tape library.
Available Modules
Links
netCDF
Mahuika
Maui_ancil
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Available Modules
module load netCDF/4.9.2-gompi-2023a
Links
netCDF-C++
Mahuika
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Available Modules
Links
netCDF-C++4
Mahuika
Maui_ancil
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Available Modules
module load netCDF-C++4/4.3.1-iimpi-2020a
module load netCDF-C++4/4.3.0-iccifort-2018.1.163-GCC-7.1.0
Links
netCDF-Fortran
Mahuika
Maui_ancil
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Available Modules
module load netCDF-Fortran/4.6.1-gompi-2023a
module load netCDF-Fortran/4.5.2-iccifort-2020.0.166
Links
nodejs
Language
Mahuika
Maui_ancil
Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
Available Modules
module load nodejs/18.18.2-GCCcore-12.3.0
module load nodejs/14.17.6-GCCcore-9.2.0
Links
nseg
Biology
Mahuika
Used to mask nucleic acid sequences
Available Modules
Links
nsync
Mahuika
nsync is a C library that exports various synchronization primitives, such as mutexes
Available Modules
Links
nullarbor
Mahuika
Reads to report pipeline for bacterial isolate NGS data.
Available Modules
Links
numactl
Mahuika
The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
Available Modules
module load numactl/2.0.16-GCCcore-12.3.0
Links
ont-guppy-gpu
Mahuika
Data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features
padloc
Mahuika
Prokaryotic Antiviral Defence LOCator
Available Modules
Links
pairtools
Mahuika
CLI tools to process mapped Hi-C data
Available Modules
Links
panaroo
Mahuika
A pangenome analysis pipeline.
Available Modules
Links
pandoc
Mahuika
Almost universal document converter
Available Modules
Links
parallel-fastq-dump
Mahuika
parallel fastq-dump wrapper
Available Modules
module load parallel-fastq-dump/0.6.6-gimkl-2020a-Python-3.8.2
parasail
Mahuika
parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.
Available Modules
Links
patchelf
Mahuika
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
Available Modules
Links
pauvre
Mahuika
Tools for plotting Oxford Nanopore and other long-read data.
Available Modules
module load pauvre/0.2.3-gimkl-2022a-Python-3.10.5
Links
pfunit
Maui
pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.
Available Modules
module load pfunit/3.2.9-CrayIntel-23.02-19
Links
pggb
Mahuika
PanGenome Graph Builder(pggb)
Available Modules
Links
pgge
Mahuika
pangenome graph evaluator
Available Modules
Links
phyx
Mahuika
phyx performs phylogenetics analyses on trees and sequences.
Available Modules
Links
picard
Biology
Mahuika
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
Available Modules
Links
pigz
Mahuika
parallel implementation of gzip,
Available Modules
Links
pixman
Mahuika
Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
Available Modules
module load pixman/0.42.2-GCC-12.3.0
Links
pod5
Mahuika
File format for storing nanopore dna data in an easily accessible way.
Available Modules
Links
pplacer
Biology
Mahuika
Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment
Available Modules
Links
preseq
Mahuika
Software for predicting library complexity and genome coverage in high-throughput sequencing.
Available Modules
Links
prodigal
Mahuika
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
Available Modules
module load prodigal/2.6.3-GCCcore-7.4.0
Links
prodigal-gv
Mahuika
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes.
Available Modules
Links
prokka
Mahuika
Prokka is a software tool for the rapid annotation of prokaryotic genomes.
Available Modules
Links
protobuf
Mahuika
Google Protocol Buffers.
Available Modules
module load protobuf/23.0-GCC-11.3.0
Links
psmc
Mahuika
Infers population size history from a diploid sequence using the PSMC model.
Available Modules
Links
pstoedit
Mahuika
Maui_ancil
pstoedit translates PostScript and PDF graphics into other vector formats.
Available Modules
module load pstoedit/3.75-GCCcore-9.2.0
module load pstoedit/3.70-GCC-7.1.0
Links
pullseq
Mahuika
Utility program for extracting sequences from a fasta/fastq file
Available Modules
Links
purge_dups
Mahuika
purge haplotigs and overlaps in an assembly based on read depth
Available Modules
Links
purge_haplotigs
Mahuika
Pipeline to help with curating heterozygous diploid genome assemblies
Available Modules
Links
pv
Mahuika
Monitors the progress of data through a unix pipeline.
Available Modules
Links
pyani
Mahuika
Whole-genome classification using Average Nucleotide Identity
Available Modules
module load pyani/0.2.12-gimkl-2022a-Python-3.10.5
Links
pycoQC
Mahuika
Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.
Available Modules
Links
pymol-open-source
Mahuika
PyMOL (open source version) molecular visualization system.
Available Modules
pyseer
Mahuika
python implementation of SEER(Sequence element enrichment analysis)
Available Modules
Links
pyspoa
Mahuika
Python bindings to spoa.
Available Modules
Links
qcat
Mahuika
Command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files
Available Modules
Links
rDock
Chemistry
Mahuika
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages.
Available Modules
Links
randfold
Mahuika
Minimum free energy of folding randomization test software
Available Modules
Links
rasusa
Mahuika
Randomly subsample sequencing reads to a specified coverage.
Available Modules
Links
razers3
Mahuika
Tool for mapping millions of short genomic reads onto a reference genome.
Available Modules
Links
rclone
Mahuika
Rclone is a command line program to sync files and directories to and from a variety of online storage services
Links
re2c
Mahuika
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
Available Modules
Links
rkcommon
Mahuika
A common set of C++ infrastructure and CMake utilities used by various components of Intel® oneAPI Rendering Toolkit.
Available Modules
Links
rnaQUAST
Mahuika
Tool for evaluating RNA-Seq assemblies using reference genome and gene database
Available Modules
Links
rsync
Maui_ancil
rsync is an open source utility that provides fast incremental file transfer. rsync is freely available under the GNU General Public License
Available Modules
Links
rust-fmlrc
Mahuika
FM-index Long Read Corrector (Rust implementation)
Available Modules
Links
samblaster
Biology
Mahuika
samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Available Modules
Links
samclip
Mahuika
Filter SAM file for soft and hard clipped alignments.
Available Modules
Links
savvy
Mahuika
Interface to various variant calling formats.
Available Modules
Links
sbt
Mahuika
sbt is a build tool for Scala, Java, and more.
Available Modules
Links
sc-RNA
Mahuika
Bioconductor bundle for single-cell RNA-Seq Data analysis
Available Modules
module load sc-RNA/2023-07-gimkl-2022a-R-bundle-Bioconductor-3.15-R-4.2.1
Links
screen_assembly
Mahuika
Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies.
Available Modules
Links
seqmagick
Biology
Mahuika
Seqmagick is a utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.
Available Modules
module load seqmagick/0.8.4-gimkl-2020a-Python-3.8.2
Links
seqtk
Biology
Mahuika
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
Available Modules
Links
shrinkwrap
Mahuika
A std::streambuf wrapper for compression formats.
Available Modules
Links
shumlib
Maui
Maui_ancil
Shumlib is the collective name for a set of libraries which are used by the UM; the UK Met Office's Unified Model, that may be of use to external tools or applications where identical functionality is desired. The hope of the project is to enable developers to quickly and easily access parts of the UM code that are commonly duplicated elsewhere, at the same time benefiting from any improvements or optimisations that might be made in support of the UM itself.
Available Modules
module load shumlib/2018.06.1-CrayIntel-23.02-19-openmp
module load shumlib/2020.01.1-iccifort-2018.1.163-GCC-7.1.0-no-openmp
Links
simuG
Mahuika
A general-purpose genome simulator
Available Modules
Links
sismonr
Mahuika
Simulation of In Silico Multi-Omic Networks R package.
Available Modules
module load sismonr/2.0.0-gimkl-2020a-R-4.1.0
Links
slow5tools
Mahuika
Toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
Available Modules
Links
smafa
Mahuika
Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length.
Available Modules
Links
smoove
Mahuika
simplifies and speeds calling and genotyping SVs for short reads.
Available Modules
Links
snakemake
Workflow_management
Mahuika
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
Available Modules
module load snakemake/8.1.0-gimkl-2022a-Python-3.11.3
Links
snaphu
Mahuika
SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping proposed by Chen and Zebker
Available Modules
Links
snappy
Mahuika
Maui_ancil
Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
Available Modules
module load snappy/1.1.10-GCCcore-12.3.0
module load snappy/1.1.9-GCCcore-9.2.0
Links
snp-sites
Mahuika
Finds SNP sites from a multi-FASTA alignment file.
Available Modules
Links
snpEff
Biology
Mahuika
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
Available Modules
somalier
Mahuika
extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF
Available Modules
Links
spaln
Mahuika
Stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.
Available Modules
Links
spdlog
Mahuika
Fast C++ logging library.
Available Modules
Links
splat
Mahuika
Maui
Splat deploys (builds and installs) the components of heterogenous systems such as cylc suites, described by splat config files, into target directory trees.
Links
spoa
Mahuika
c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences
Available Modules
Links
sratoolkit
Biology
Mahuika
srun-wrapper
Mahuika
Maui
sublime
Mahuika
Maui
Text editor with GUI
Links
swarm
Biology
Mahuika
A robust and fast clustering method for amplicon-based studies. The purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons. Results of traditional clustering algorithms are strongly input-order dependent, and rely on an arbitrary global clustering threshold. swarm results are resilient to input-order changes and rely on a small local linking threshold d, representing the maximum number of differences between two amplicons.
Available Modules
Links
swissknife
Mahuika
Perl module for reading and writing UniProtKB data in plain text format.
Available Modules
Links
tRNAscan-SE
Mahuika
Transfer RNA detection
Available Modules
Links
tabix
Mahuika
Generic indexer for TAB-delimited genome position files
Available Modules
Links
tabixpp
Mahuika
C++ wrapper to tabix indexer
Available Modules
Links
tbb
Mahuika
Maui_ancil
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.
Available Modules
module load tbb/2021.5.0-GCC-11.3.0
module load tbb/2019-GCC-7.1.0
Links
tbl2asn
Mahuika
Command-line program that automates the creation of sequence records for submission to GenBank
Available Modules
Links
tmux
Mahuika
tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.
Available Modules
Links
trf
Biology
Mahuika
Locates tandem repeats in DNA sequences.
Links
trimAl
Mahuika
Tool for automated alignment trimming in large-scale phylogenetic analyses
Available Modules
Links
um2netcdf
Maui_ancil
um2netcdf converts Unified Model output files in fieldsfile format into netCDF format.
Available Modules
Links
unimap
Mahuika
Fork of minimap2 optimized for assembly-to-reference alignment.
Available Modules
Links
unrar
Mahuika
RAR is a powerful archive manager.
Available Modules
Links
util-linux
Mahuika
Set of Linux utilities
Available Modules
Links
vcflib
Mahuika
Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.
Available Modules
Links
verkko
Mahuika
Hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads
Available Modules
Links
vg
Mahuika
variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
Available Modules
Links
wgsim
Mahuika
Wgsim is a small tool for simulating sequence reads from a reference genome.
Available Modules
Links
wheel
Mahuika
A built-package format for Python.
Available Modules
module load wheel/0.31.1-gimkl-2020a-Python-2.7.18
Links
wtdbg
Mahuika
de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.
Available Modules
Links
wxWidgets
Mahuika
widget toolkit and tools library for creating graphical user interfaces for cross-platform applications.
Available Modules
Links
x264
Mahuika
x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
Available Modules
module load x264/20220620-GCC-11.3.0
Links
x265
Mahuika
x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.
Available Modules
Links
xkbcommon
Mahuika
keyboard keymap compiler and support library
Available Modules
Links
xtb
Mahuika
xtb - An extended tight-binding semi-empirical program package.
Available Modules
Links
yacrd
Mahuika
Chimeric Read Detector for long reads
Available Modules
Links
yajl
Mahuika
Yet Another JSON Library. Why does the world need another C library for parsing JSON? Good question.
Available Modules
Links
yak
Mahuika
Yet another k-mer analyzer
Available Modules
Links
yaml-cpp
Mahuika
YAML parser and emitter in C++
Available Modules
module load yaml-cpp/0.8.0-GCC-12.3.0
Links
zlib
Mahuika
Maui
Maui_ancil
zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
Available Modules
module load zlib/1.2.13
module load zlib/1.2.11-CrayIntel-23.02-19
module load zlib/1.2.11
Links
zstd
Mahuika
Maui_ancil
Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.
Available Modules
module load zstd/1.5.5-GCCcore-12.3.0
module load zstd/1.5.2-GCCcore-9.2.0