Supported Applications

For more information on environment-modules see Finding Software.

On Mahuika, and Ancillary nodes (both Mahuika and Māui) software packages are provided using 'Lmod' an implementation of Environment Modules with additional features.
A list of available software can be obtained with the module spider command.

On Māui (XC50), software packages are provided using traditional Environment Modules. No modules are loaded by default.
A list of available software can be obtained with the module avail command.

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

Available Modules

module load ABAQUS/2020
Links
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%
University of Waikato 96%

Mass screening of contigs for antimicrobial and virulence genes

Available Modules

module load ABRicate/1.0.0-GCC-11.3.0-Perl-5.34.1
Links

AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates

Available Modules

module load abritamr/1.0.14-gimkl-2022a-Python-3.11.3
Links

Collection of C++ library code designed to augment the C++ standard library.

Available Modules

module load Abseil/20230125.3-GCC-11.3.0
Links

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Available Modules

module load ABySS/2.2.5-gimpi-2020a
Links

ACTC converts independent triangles into triangle strips or fans.

Available Modules

module load ACTC/1.1-GCCcore-9.2.0
Links

Ssearches for and removes remnant adapter sequences from High-Throughput Sequencing data.

Available Modules

module load AdapterRemoval/2.3.1-GCCcore-7.4.0
Links

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

module load AdaptiveCpp/23.10.0-GCC-12.3.0-CUDA-12.2.2
Links

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

module load Advisor/2020_update1
Links

Suite of tools to handle gene annotations in any GTF/GFF format.

Available Modules

module load AGAT/1.0.0-gimkl-2022a-Perl-5.34.1-R-4.2.1
Links

Alignment of sequences with structural variants.

Available Modules

module load AGE/2017-GCC-7.4.0-serial
Links

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known

Available Modules

module load AlphaFold/2.3.2
Links

AlphaFold2 databases

Available Modules

module load AlphaFold2DB/2022-06
Links

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

module load AlwaysIntelMKL/1.0
Links

Collection of tools for genome assembly

Available Modules

module load AMOS/3.1.0-GCC-11.3.0
Links

NCBI Antimicrobial Resistance Gene Finder Plus

Available Modules

module load AMRFinderPlus/3.10.45-GCC-11.3.0
Links

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

module load Anaconda3/2021.05-gimkl-2020a

Warning

Warning: Anaconda is deprecated for license reasons. Please switch to using Miniforge3 for any new environments.

Links

Program for analysing NGS data.

Available Modules

module load angsd/0.935-GCC-9.2.0
Links

Calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes.

Available Modules

module load ANIcalculator/1.0-GCC-11.3.0
Links

Efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes .

Available Modules

module load ANNOVAR/2020Oct01-GCC-9.2.0-Perl-5.30.1
Links

A bundle of computer-aided engineering software including Fluent and CFX.

Available Modules

module load ANSYS/19.2
Links
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 88%
Orbis Diagnostics 100%
Auckland University of Technology Faculty of Engineering 88%
University of Waikato 88%
University of Canterbury 99%
University of Otago 99%

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

module load ant/1.10.9-Java-1.8.0_144
Links

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/5.1.2-gimkl-2020a-Python-3.8.2
Links

ANother Tool for Language Recognition

Available Modules

module load ANTLR/2.7.7-GCC-7.4.0

Warning

Warning: ANTLR/2.7.7-GCC-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

Available Modules

module load ANTs/2.3.5-gimkl-2020a
Links

Convert various sequence formats to FASTA

Available Modules

module load any2fasta/0.4.2-GCC-11.3.0
Links

AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

Available Modules

module load AOCC/4.0.0-GCC-11.3.0
Links

Optimized version of BLIS for AMD EPYC family of processors..

Available Modules

module load AOCL-BLIS/4.0-GCC-11.3.0
Links

Optimized version of FFTW for AMD EPYC family of processors.

Available Modules

module load AOCL-FFTW/4.0-gompi-2022a
Links

Optimized version of ScaLAPACK for AMD EPYC family of processors.

Available Modules

module load AOCL-ScaLAPACK/4.0-gompi-2022a
Links

Apptainer is a portable application stack packaging and runtime utility.

Available Modules

module load Apptainer/1.2.5
Links

Apache Portable Runtime (APR) libraries.

Available Modules

module load APR/1.6.5
Links

Apache Portable Runtime (APR) util libraries.

Available Modules

module load APR-util/1.6.1

Warning

Warning: APR-util/1.6.1 is old and marked for deletion. If you still need it, then please let us know.

Links

Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

Available Modules

module load argtable/2.13-GCC-11.3.0
Links

aria2 is a lightweight multi-protocol & multi-source command-line download utility.

Available Modules

module load aria2/1.36.0-GCCcore-11.3.0
Links

Antimicrobial Resistance Identification By Assembly

Available Modules

module load ARIBA/2.14.6-gimkl-2022a-Python-3.10.5
Links

C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.

Available Modules

module load Armadillo/10.5.3-gimkl-2020a
Links

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

Available Modules

module load arpack-ng/3.6.3-intel-2017a

Warning

Links

Apache Arrow, a cross-language development platform for in-memory data.

Available Modules

module load Arrow/8.0.0-GCCcore-11.3.0
Links

a pArallel Server for Adaptive GeoInformation

Available Modules

module load ASAGI/20240327-foss-2023a
Links

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

module load Aspera-CLI/3.9.6.1467.159c5b1
Links

AT-SPI 2 toolkit bridge

Available Modules

module load at-spi2-atk/2.38.0-GCCcore-9.2.0
Links

Assistive Technology Service Provider Interface.

Available Modules

module load at-spi2-core/2.38.0-GCCcore-9.2.0
Links

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.

Available Modules

module load ATK/2.36.0-GCCcore-9.2.0
Links

Commands for Manipulating Filesystem Extended Attributes

Available Modules

module load attr/2.5.1-GCCcore-9.2.0
Links

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

Available Modules

module load AUGUSTUS/3.4.0-gimkl-2020a
Links

A collection of more than 500 macros for GNU Autoconf

Available Modules

module load Autoconf-archive/2023.02.20
Links

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

module load AutoDock-GPU/1.5.3-GCC-11.3.0-CUDA-11.6.2
Links

AutoDock Vina is an open-source program for doing molecular docking.

Available Modules

module load AutoDock_Vina/1.1.2_linux_x86
Links

Java Development Kit (JDK), and a compliant implementation of the Java Standard Edition (SE) specification.

Available Modules

module load azul-zulu/17.36.19-jdk-17.0.4.1
Links

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Available Modules

module load BamTools/2.5.1-gimkl-2018b
Links

Repository that contains several programs that perform operations on SAM/BAM files.

Available Modules

module load bamUtil/1.0.15
Links

Bandage is a program for visualising de novo assembly graphs

Available Modules

module load Bandage/0.8.1_Centos
Links

Barrnap predicts the location of ribosomal RNA genes in genomes.

Available Modules

module load barrnap/0.9-GCC-9.2.0
Links

Basilisk is a Free Software program for the solution of partial differential equations on adaptive Cartesian meshes.

Available Modules

module load Basilisk/20180226-gimpi-2018b

Warning

Links

Program for inference of recent immigration rates between populations using unlinked multilocus genotypes

Available Modules

module load BayesAss/3.0.4-GCC-9.2.0
Links

Identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Available Modules

module load BayeScan/2.1-GCCcore-7.4.0
Links

Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables

Available Modules

module load BayPass/2.31-intel-2022a
Links

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/3.4.1-GCCcore-9.2.0

Warning

Warning: Bazel/3.7.2-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

BBMap short read aligner, and other bioinformatic tools.

Available Modules

module load BBMap/38.95-gimkl-2020a
Links

Manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

Available Modules

module load BCFtools/1.12-GCC-9.2.0

Warning

Links

Converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files

Available Modules

module load BCL-Convert/4.0.3

Warning

Links

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

module load bcl2fastq2/2.20.0-gimkl-2018b
Links

Package for phasing genotypes and for imputing ungenotyped markers.

Available Modules

module load Beagle/5.0-12Jul19.0df
Links

beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

Available Modules

module load beagle-lib/3.0.1-gimkl-2017a

Warning

Links

Bayesian MCMC phylogenetic analysis of molecular sequences for reconstructing phylogenies and testing evolutionary hypotheses.

Available Modules

module load BEAST/2.6.6
Links

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

module load BEDOPS/2.4.41-gimkl-2022a
Links

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/2.31.1-GCC-12.3.0
Links

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-2020a
Links

Bam Error Stats Tool (best): analysis of error types in aligned reads

Available Modules

module load best/0.1.0
Links

Collection of code for Bayesian genomic cline analyses.

Available Modules

module load BGC-Bayesian-genomic-clines/1.03-gompi-2023a
Links

Highly parallel construction, indexing and querying of colored and compacted de Bruijn graphs.

Available Modules

module load Bifrost/1.0.4-GCC-9.2.0

Warning

Links

Constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).

Available Modules

module load BiG-SCAPE/1.1.5-gimkl-2022a-Python-3.11.3
Links

binutils: GNU binary utilities

Available Modules

module load binutils/2.26-GCCcore-5.4.0
Links

Read BigWig and BigBed genome feature databases

Available Modules

module load Bio-DB-BigFile/1.07-GCC-9.2.0-Perl-5.30.1-mt
Links

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

An extension to awk, adding the support of several common biological data formats

Available Modules

module load bioawk/1.0
Links

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

module load BioPP/2.4.1-GCC-9.2.0
Links

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Available Modules

module load Bismark/0.22.3-gimkl-2018b
Links

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

Available Modules

module load Bison/3.0.4-GCC-5.4.0
Links

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/2.9.0-gimkl-2018b
Links

BLAST databases downloaded from NCBI.

Available Modules

module load BLASTDB/2024-07
Links

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

Available Modules

module load BLAT/3.5-gimkl-2018b

Warning

Warning: BLAT/3.5-gimkl-2018b is old and marked for deletion. Please select a more recent version (try 'module spider BLAT') or let us know that you still need it.

Links

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

module load BlenderPy/2.93.1-gimkl-2020a-Python-3.9.5

Warning

Warning: BlenderPy/2.93.1-gimkl-2020a-Python-3.9.5 is old and marked for deletion. If you still need it, then please let us know.

Links

BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

Available Modules

module load BLIS/0.9.0-GCC-11.3.0
Links

The BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis

Available Modules

module load BOLT-LMM/2.4
Links

Boost provides free peer-reviewed portable C++ source libraries.

Available Modules

module load Boost/1.76.0-intel-2022a
Links

Ultrafast, memory-efficient short read aligner.

Available Modules

module load Bowtie/0.12.8
Links

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Available Modules

module load Bowtie2/2.4.1-GCC-9.2.0
Links

A platform for running big bioinformatics jobs that consist of a series of processing stages

Available Modules

module load Bpipe/0.9.9.8

Warning

Warning: Bpipe/0.9.9.8 is old and marked for deletion. If you still need it, then please let us know.

Links

Hghly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Available Modules

module load Bracken/2.6.0-GCCcore-9.2.0

Warning

Links

BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

Available Modules

module load BRAKER/2.1.6-gimkl-2020a-Perl-5.30.1-Python-3.8.2

Warning

Links

Nucleotide-resolution analysis of structural variants

Available Modules

module load BreakSeq2/2.2-gimkl-2018b-Python-2.7.16

Warning

Warning: BreakSeq2/2.2-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

breseq is a computational pipeline for the analysis of short-read re-sequencing data

Available Modules

module load breseq/0.35.4-gimkl-2020a-R-4.0.1

Warning

Links

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

module load bsddb3/6.2.6-gimkl-2018b-Python-2.7.16

Warning

Warning: bsddb3/6.2.6-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Available Modules

module load BUSCO/4.0.5-gimkl-2020a
Links

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/0.7.15-gimkl-2017a

Warning

Links

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-9.2.0
Links

c-ares is a C library for asynchronous DNS requests (including name resolves)

Available Modules

module load c-ares/1.18.1-GCCcore-11.3.0
Links

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/1.16.0-GCCcore-9.2.0
Links

Sequence assembler designed for high-noise single-molecule sequencing.

Available Modules

module load Canu/2.2-GCC-11.3.0
Links

Fast data interchange format and capability-based RPC system.

Available Modules

module load CapnProto/0.8.0-GCCcore-9.2.0
Links

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

module load Catch2/2.13.4

Warning

Warning: Catch2/2.13.4 is old and marked for deletion. If you still need it, then please let us know.

Links

Clozure CL (often called CCL for short) is a free Common Lisp implementation

Available Modules

module load CCL/1.12-GCCcore-9.2.0

Warning

Warning: CCL/1.12-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

Available Modules

module load CD-HIT/4.8.1-GCC-11.3.0
Links

Fasta file indexing and retrival tool

Available Modules

module load cdbfasta/0.99-GCC-11.3.0
Links

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

Available Modules

module load CDO/1.9.8-gimpi-2020a
Links

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.

Available Modules

module load CellRanger/6.1.2
Links

Classifier for metagenomic sequences

Available Modules

module load Centrifuge/1.0.4.1-GCC-12.3.0
Links

C++11 serialization library

Available Modules

module load Cereal/1.3.0
Links

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

module load CFITSIO/3.45-GCCcore-7.4.0
Links

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/4.13-GCCcore-7.4.0
Links

Nvidia and AMD GPU utility for SeisSol.

Available Modules

module load chainforge/0.0.3-foss-2023a-Python-3.11.6
Links

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

Rapid assessment of genome bin quality using machine learning

Available Modules

module load CheckM2/1.0.1-Miniconda3
Links

Assess the quality of metagenome-assembled viral genomes.

Available Modules

module load CheckV/0.6.0-gimkl-2020a-Python-3.8.2

Warning

Links

A complete suite for gene-by-gene schema creation and strain identification..

Available Modules

module load chewBBACA/3.1.2-gimkl-2022a-Python-3.11.3
Links

Rust implementation of NanoFilt+NanoLyse

Available Modules

module load chopper/0.5.0-GCC-11.3.0
Links

A tool to circularize genome assemblies

Available Modules

module load Circlator/1.5.5-gimkl-2022a-Python-3.10.5
Links

Package for visualizing data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Available Modules

module load Circos/0.69-9-GCC-9.2.0
Links

Syumphonizing pileup and full-alignment for high-performance long-read variant calling.

Available Modules

module load Clair3/0.1.12-Miniconda3
Links

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.

Available Modules

module load Clang/17.0.6-GCC-12.3.0-CUDA-12.2.2
Links

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

module load Clustal-Omega/1.2.4-GCC-11.3.0
Links

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

Available Modules

module load ClustalW2/2.1-gimkl-2017a

Warning

Warning: ClustalW2/2.1-gimkl-2017a was built with an old compiler and will soon be removed. Please switch to using ClustalW2/2.1-GCC-11.3.0 instead, or even better switch to newer tools such as MUSCLE or MAFFT for DNA alignments, or Clustal-Omega for protein alignments

Links

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
Links

Copy Number Variation discovery and genotyping from depth of read mapping.

Available Modules

module load CNVnator/0.4-GCC-7.4.0
Links

Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped read

Available Modules

module load CNVpytor/1.0-gimkl-2020a-Python-3.8.2
Links

code-server for OpenOnDemand

Available Modules

module load code-server/4.92.2
Links

faster and more accurate reimplementation of BUSCO.

Available Modules

module load compleasm/0.2.6-gimkl-2022a
Links

COMSOL is a multiphysics solver that provides a unified workflow for electrical, mechanical, fluid, and chemical applications.

Available Modules

module load COMSOL/5.6
Links
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%

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

Clusters contigs and counts reads from de novo assembled transcriptomes.

Available Modules

module load Corset/1.09-GCC-9.2.0

Warning

Warning: Corset/1.09-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

DNA read coverage and relative abundance calculator focused on metagenomics applications

Available Modules

module load CoverM/0.7.0-GCC-12.3.0
Links

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

The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.

Available Modules

module load CPMD/4.3-foss-2023a
Links

C++ port of the JUnit framework for unit testing.

Available Modules

module load CppUnit/1.13.2-GCCcore-7.4.0

Warning

Warning: CppUnit/1.15.1-GCCcore-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Creating Reference databases for Amplicon-Based Sequencing.

Available Modules

module load CRABS/1.0.6
Links

A tool for quick quality assessment of cram and bam files, intended for long read sequencing

Available Modules

module load CRAMINO/0.9.7-GCC-11.3.0
Links

Workflow Management System geared towards scientific workflows.

Available Modules

module load cromwell/84-Java-1.8.0_144
Links

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

module load ctags/5.8

Warning

Warning: ctags/5.8 is old and marked for deletion. If you still need it, then please let us know.

Links

ctffind is a program for finding CTFs of electron micrographs

Available Modules

module load ctffind/4.1.10
Links

C++ Thread Pool Library

Available Modules

module load CTPL/0.0.2

Warning

Warning: CTPL/0.0.2 is old and marked for deletion. If you still need it, then please let us know.

Links

Cube general purpose C++ library component and command-line tools.

Available Modules

module load CubeLib/4.4.4-GCCcore-9.2.0
Links

Cube high-performance C writer library component.

Available Modules

module load CubeWriter/4.5-GCCcore-9.2.0
Links

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.

Available Modules

module load CUDA/11.0.2
Links

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

Available Modules

module load cuDNN/7.6.4.38-CUDA-10.1.243
Links

Transcript assembly, differential expression, and differential regulation for RNA-Seq

Available Modules

module load Cufflinks/2.2.1-gimkl-2017a
Links

Automated testing framework for C.

Available Modules

module load CUnit/2.1-3-GCCcore-9.2.0

Warning

Warning: CUnit/2.1-3-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

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
Links

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/1.16-gimkl-2018b-Python-3.7.3
Links

Fast and scalable long-read-based SV detection

Available Modules

module load cuteSV/2.0.2-gimkl-2020a-Python-3.8.2
Links

Common Workflow Language tool description reference implementation

Available Modules

module load cwltool/3.0.20200317203547-gimkl-2020a-Python-3.8.2

Warning

Warning: cwltool/3.0.20200317203547-gimkl-2020a-Python-3.8.2 is old and marked for deletion. If you still need it, then please let us know.

Links

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.

Available Modules

module load Cytoscape/2.7.0

Warning

Links

cython + htslib == fast VCF and BCF processing

Available Modules

module load cyvcf2/0.30.11-gimkl-2020a-Python-3.8.2
Links

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

Diffusion Approximation for Demographic Inference

Available Modules

module load dadi/2.3.0-gimkl-2022a-Python-3.11.3
Links

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

module load DaliLite/5.0-iimpi-2020a

Warning

Warning: DaliLite/5.0-iimpi-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

de novo transcriptome annotator..

Available Modules

module load dammit/1.2

Warning

Warning: dammit/1.2 is old and marked for deletion. If you still need it, then please let us know.

Links

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

module load DAS_Tool/1.1.5-gimkl-2022a-R-4.2.1
Links

Tool to gather data from across NCBI databases

Available Modules

module load datasets/15.29.0
Links

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

Available Modules

module load DB/6.2.23-GCCcore-7.4.0
Links

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

module load DBus/1.13.8-GCCcore-7.4.0
Links

A tool that can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

Available Modules

module load DeconSeq/0.4.3
Links

Efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks.

Available Modules

module load DeepLabCut/2.3.5
Links

Available Modules

module load DeePMD-kit/2.1.1
Links

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

module load deepTools/3.2.1-gimkl-2018b-Python-3.7.3
Links

Integrated simulation of sediment transport and morphology, waves, water quality and ecology.

Available Modules

module load Delft3D/141732-intel-2022a
Links

3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments

Available Modules

module load Delft3D_FM/68673-intel-2020a
Links

Structural variant discovery by integrated paired-end and split-read analysis

Available Modules

module load Delly/1.1.3
Links

R functions that simplify and expedite common tasks in package development.

Available Modules

module load devtools/2.4.4-gimkl-2022a-R-4.2.1
Links

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

Available Modules

module load DFT-D4/3.5.0-foss-2023a
Links

Sequence aligner for protein and translated DNA searches

Available Modules

module load DIAMOND/2.1.9-GCC-11.3.0
Links

Assembler suitable for large genomes based on Illumina reads of length 250 or longer.

Available Modules

module load DISCOVARdenovo/52488

Warning

Warning: DISCOVARdenovo/52488 is old and marked for deletion. If you still need it, then please let us know.

Links

High-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Available Modules

module load Dorado/0.3.2
Links

Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.

Available Modules

module load double-conversion/3.2.1-GCC-11.3.0

Warning

Warning: double-conversion/3.2.1-GCC-11.3.0 is old and marked for deletion. Please select a more recent version (try 'module spider double-conversion') or let us know that you still need it.

Links

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

module load Doxygen/1.8.17-GCCcore-9.2.0
Links

Tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs..

Available Modules

module load DRAM/1.3.5-Miniconda3
Links

Rapid and accurate comparison and de-replication of microbial genomes

Available Modules

module load drep/2.3.2-gimkl-2018b-Python-3.7.3
Links

Fast calculation of the ABBA-BABA statistics across many populations/species

Available Modules

module load Dsuite/20210718-intel-compilers-2022.0.2
Links

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

module load dtcmp/1.1.3-gimpi-2020a
Links

uphold your DUP and DEL calls

Available Modules

module load duphold/0.2.3
Links

Range of tools to support operations on Duplex Sequencing read pairs.

Available Modules

module load duplex-tools/0.2.20-gimkl-2022a-Python-3.10.5
Links

easi is a library for the Easy Initialization of models in three (or less or more) dimensional domains.

Available Modules

module load easi/1.3.0-foss-2023a
Links

Available Modules

module load EasyBuild/4.9.2
Links

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/2.17.0-gimpi-2020a
Links

Standalone versatile serotyping module for Escherichia coli..

Available Modules

module load ectyper/1.0.0-gimkl-2022a-Python-3.10.5
Links

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.

Available Modules

module load edlib/1.3.8.post2-gimkl-2020a-Python-3.8.2
Links

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

module load eDNA/2021.11-gimkl-2020a-Python-3.8.2
Links

Automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

Available Modules

module load EDTA/2.1.0
Links

Tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments

Available Modules

module load eggnog-mapper/2.0.1b-gimkl-2020a-Python-2.7.18
Links

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

Available Modules

module load Eigen/3.3.9
Links

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

module load EIGENSOFT/7.2.1-gimkl-2018b
Links

Eigenvalue SoLvers for Petaflop-Applications .

Available Modules

module load ELPA/2023.11.001-foss-2023a
Links

Greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes

Available Modules

module load EMAN2/2.99.47-gpu
Links

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

module load EMBOSS/6.6.0-gimkl-2020a
Links

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/3.5.1-GCCcore-7.4.0
Links

Tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly

Available Modules

module load emmtyper/0.2.0-gimkl-2022a-Python-3.11.3
Links

R package for integrated construction of Ecological Niche Models.

Available Modules

module load ENMTML/2021-06-24-gimkl-2020a-R-4.1.0

Warning

Warning: ENMTML/2021-06-24-gimkl-2020a-R-4.1.0 is old and marked for deletion. If you still need it, then please let us know.

Links

C++ header-only library for numerical optimization

Available Modules

module load ensmallen/2.17.0-gimkl-2020a
Links

an advanced method for accessing the NCBI's set of interconnected databases such as publication, sequence, structure, gene, variation, expression, etc.

Available Modules

module load entrez-direct/13.3
Links

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
Links

A Python framework for the analysis and visualization of phylogenetic trees

Available Modules

module load ETE/3.1.1-gimkl-2018b-Python-3.7.3
Links

Completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. Also condatains smetana, carveme and memote .

Available Modules

module load EukRep-EukCC/0.6.7-2.1.0-Miniconda3
Links

Bayesian tree inference, particularly suitable for large-scale analyses.

Available Modules

module load ExaBayes/1.5.1-gimpi-2020a
Links

Exascale Maximum Likelihood for phylogenetic inference using MPI.

Available Modules

module load ExaML/3.0.22-gimkl-2020a
Links

Generic tool for pairwise sequence comparison

Available Modules

module load exonerate/2.4.0-GCC-9.2.0
Links

Tool for estimating repeat sizes

Available Modules

module load ExpansionHunter/5.0.0
Links

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/2.2.9-GCCcore-9.2.0
Links

Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches

Available Modules

module load Extrae/3.8.3-intel-2020a

Warning

Warning: Extrae/3.8.3-intel-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

Falcon: a set of tools for fast aligning long reads for consensus and assembly

Available Modules

module load FALCON/1.8.8-gimkl-2020a-Python-2.7.18
Links

Tool for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).

Available Modules

module load FastANI/1.33-intel-2020a
Links

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

Available Modules

module load FastME/2.1.6.1-gimkl-2018b
Links

A tool designed to provide fast all-in-one preprocessing for FastQ files.

Available Modules

module load fastp/0.20.0-GCCcore-7.4.0
Links

A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

Available Modules

module load fastq-tools/0.8-gimkl-2017a

Warning

Warning: fastq-tools/0.8-gimkl-2017a is old and will soon be removed. Please let us know if you would like a new version of fastq-tools to be installed.

Links

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

module load FastQ_Screen/0.15.1-GCC-9.2.0-Perl-5.30.1
Links

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

Available Modules

module load FastQC/0.12.1
Links

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

module load fastStructure/1.0-gimkl-2020a-Python-2.7.18
Links

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-GCC-12.3.0
Links

Tools for Short-Reads FASTA/FASTQ files preprocessing.

Available Modules

module load FASTX-Toolkit/0.0.14-GCC-11.3.0
Links

Format converting tool for genotype Data.

Available Modules

module load fcGENE/1.0.7

Warning

Warning: fcGENE/1.0.7 is old and marked for deletion. If you still need it, then please let us know.

Links

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-GCC-12.3.0
Links

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/6.7.5-1526-intel-2020a

Warning

Links

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
Links

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-GCC-12.3.0
Links

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.MPI/3.3.10-gompi-2023a
Links

A set of tools to analyze genomic data with a focus on Next Generation Sequencing.

Available Modules

module load fgbio/2.0.2

Warning

Warning: fgbio/2.0.2 is old and marked for deletion. If you still need it, then please let us know.

Links

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.

Available Modules

module load FIGARO/1.1.2-gimkl-2022a-Python-3.11.3
Links

A Perl version of the rename utility, with support for regular expressions.

Available Modules

module load File-Rename/1.13-GCC-9.2.0
Links

Send large files quickly and securely using REANNZ FileSender.

Available Modules

module load FileSender/2.49.0-foss-2023a
Links

Tool for filtering long reads by quality.

Available Modules

module load Filtlong/0.2.0
Links

Identifies the FimH type in total or partial sequenced isolates of E. coli..

Available Modules

module load FimTyper/1.0.1-GCC-11.3.0-Perl-5.34.1

Warning

Warning: FimTyper/1.0.1-GCC-11.3.0-Perl-5.34.1 is old and marked for deletion. If you still need it, then please let us know.

Links

A package for population structure inference from RAD-seq data

Available Modules

module load fineRADstructure/0.3.2r109-GCCcore-7.4.0

Warning

Links

Population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence dat

Available Modules

module load fineSTRUCTURE/4.1.1-gimkl-2022a-Perl-5.34.1
Links

FlatBuffers: Memory Efficient Serialization Library

Available Modules

module load flatbuffers/2.0.0-GCCcore-9.2.0

Warning

Warning: flatbuffers/2.0.0-GCCcore-9.2.0 is old and marked for deletion. Please select a more recent version (try 'module spider flatbuffers') or let us know that you still need it.

Links

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

Available Modules

module load flex/2.6.0-GCC-5.4.0
Links

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

module load FlexiBLAS/3.3.1-GCC-12.3.0
Links

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

module load FLTK/1.3.5-GCCcore-9.2.0
Links

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/2.9.5-foss-2023a-Python-3.11.6
Links

Tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data

Available Modules

module load fmlrc/1.0.0-GCC-9.2.0

Warning

Warning: fmlrc/1.0.0-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Formatting library providing a fast and safe alternative to C stdio and C++ iostreams.

Available Modules

module load fmt/8.0.1
Links

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

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.

Available Modules

module load forge/21.1.3
Links

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

Available Modules

module load foss/2022a
Links

FragGeneScan is an application for finding (fragmented) genes in short reads.

Available Modules

module load FragGeneScan/1.31-gimkl-2018b
Links

Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.

Available Modules

module load FreeBayes/1.3.2-GCC-9.2.0
Links

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

Available Modules

module load FreeSurfer/7.2.0-centos7_x86_64
Links

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/2.11.1-GCCcore-11.3.0
Links

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Available Modules

module load FreeXL/1.0.2-gimkl-2017a
Links

Free Implementation of the Unicode Bidirectional Algorithm.

Available Modules

module load FriBidi/1.0.12-GCC-12.3.0
Links

FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.

Available Modules

module load FTGL/2.1.3-rc5-GCCcore-7.4.0
Links

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/1.0.2-gimkl-2020a-Python-3.9.9

Warning

Links

Extract sequences from a fastx (fasta or fastq) file given a subsequence.

Available Modules

module load fxtract/2.4-GCC-11.3.0
Links

Library contains GRIB2 encoder/decoder ('C' version).

Available Modules

module load g2clib/1.6.0-GCC-12.3.0
Links

Library contains GRIB2 encoder/decoder and search/indexing routines.

Available Modules

module load g2lib/3.2.0-GCC-12.3.0
Links

A reference implementation of the GA4GH API

Available Modules

module load ga4gh/0.3.6-gimkl-2020a-Python-2.7.18

Warning

Warning: ga4gh/0.3.6-gimkl-2020a-Python-2.7.18 is old and marked for deletion. If you still need it, then please let us know.

Links

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

module load GATK/3.8-1
Links

Available Modules

module load Gaussian/09-C.01

Warning

Links
Licence

Gaussian is proprietary software.

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,...).

Available Modules

module load GCC/5.4.0
Links

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,...).

Available Modules

module load GCCcore/5.4.0
Links

Libraries and tools for interacting with Google Cloud products and services.

Available Modules

module load gcloud/485.0.0
Links

Interface to Gd Graphics Library

Available Modules

module load GD/2.76-GCC-11.3.0-Perl-5.34.1
Links

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/2.2.2-gimkl-2017a-GEOS-3.5.1
Links

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

module load Gdk-Pixbuf/2.42.8-GCC-11.3.0
Links

Available Modules

module load geany/1.35
Links

Genome-wide Efficient Mixed Model Association

Available Modules

module load GEMMA/0.98.5-GCC-12.3.0
Links

GPU-GEMM generator for the Discontinuous Galerkin method.

Available Modules

module load gemmforge/0.0.207-foss-2023a-Python-3.11.6
Links

Eukaryotic gene prediction suite with automatic training

Available Modules

module load GeneMark-ES/4.71-GCC-11.3.0
Links

GenomeThreader is a software tool to compute gene structure predictions.

Available Modules

module load GenomeThreader/1.7.3-Linux_x86_64-64bit
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GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations.

Available Modules

module load genometools/1.6.1-GCCcore-7.4.0
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Generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.

Available Modules

module load GenoVi/0.2.16-Miniconda3
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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
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Toolkit to assemble organelle genome from genomic skimming data.

Available Modules

module load GetOrganelle/1.7.7.0-gimkl-2022a
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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/0.19.8.1
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single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Available Modules

module load gfastats/1.3.6-GCC-11.3.0
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GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

Available Modules

module load gffread/0.12.7-GCC-11.3.0
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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

module load giflib/5.2.1-GCCcore-9.2.0
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GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL

Available Modules

module load gimkl/2018b
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GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.

Available Modules

module load gimpi/2018b
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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

module load git/2.23.3
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GLib is one of the base libraries of the GTK+ project

Available Modules

module load GLib/2.53.7-GCCcore-7.4.0
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Gene finder based on a Generalized Hidden Markov Model.

Available Modules

module load GlimmerHMM/3.0.4c-GCC-9.2.0
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OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.

Available Modules

module load GLM/0.9.9.8
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Client for the Globus Flows service.

Available Modules

module load globus-automate-client/0.16.1.post1-gimkl-2022a
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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/2.24.0-gimkl-2022a-Python-3.10.5
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GNU Linear Programming Kit is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.

Available Modules

module load GLPK/5.0-GCCcore-11.3.0
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GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

Available Modules

module load GMAP-GSNAP/2021-12-17-GCC-11.3.0
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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
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Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor..

Available Modules

module load gmsh/2.0.2-Miniconda3
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Portable interactive, function plotting utility

Available Modules

module load gnuplot/5.4.2-GCC-7.4.0
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An open source programming language

Available Modules

module load Go/1.11.5

Warning

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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

module load GObject-Introspection/1.72.0-GCC-11.3.0

Warning

Warning: GObject-Introspection/1.72.0-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

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A genetic algorithm for docking flexible ligands into protein binding sites

Available Modules

module load GOLD/2020

Warning

Links
Licence

GOLD is proprietary software.

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

Available Modules

module load gompi/2022a
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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

module load google-sparsehash/2.0.3-gimkl-2018b
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Google's C++ test framework

Available Modules

module load googletest/1.10.0-GCCcore-9.2.0
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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

module load GPAW/24.1.0-foss-2023a
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GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

Available Modules

module load gperf/3.1-GCCcore-7.4.0
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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

module load Graphviz/2.42.2-GCC-9.2.0
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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

module load GRASS/7.6.1-gimkl-2018b-Python-2.7.16
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GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Available Modules

module load GRIDSS/2.13.2-gimkl-2020a
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Command line tool for Google Drive.

Available Modules

module load grive2/0.5.1-GCCcore-9.2.0

Warning

Warning: grive2/0.5.1-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

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. This is a GPU enabled build, containing both MPI and threadMPI binaries.

Available Modules

module load GROMACS/2020.5-intel-2020a-cuda-11.0.2-hybrid
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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
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Tool to sort genomic files according to a genomefile.

Available Modules

module load gsort/0.1.4

Warning

Warning: gsort/0.1.4 is old and marked for deletion. If you still need it, then please let us know.

Links

GStreamer plug-ins and elements.

Available Modules

module load GST-plugins-base/1.16.2-GCC-9.2.0
Links

library for constructing graphs of media-handling components..

Available Modules

module load GStreamer/1.16.2-GCC-9.2.0
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A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Available Modules

module load GTDB-Tk/2.1.0-gimkl-2020a-Python-3.9.9
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GTK+ is the primary library used to construct user interfaces in GNOME.

Available Modules

module load GTK+/3.24.23-GCC-9.2.0
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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
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Genealogies Unbiased By recomBinations In Nucleotide Sequences

Available Modules

module load Gubbins/3.2.2-gimkl-2022a-Python-3.10.5
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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-Python-3.11.3
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A simple C++17 wrapper for HDF5.

Available Modules

module load h5pp/1.9.0-gimpi-2020a
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Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content

Available Modules

module load haplocheck/1.3.3
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HarfBuzz is an OpenType text shaping engine.

Available Modules

module load HarfBuzz/4.4.1-GCC-11.3.0
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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/4.2.15-GCCcore-9.2.0
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HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Available Modules

module load HDF5/1.12.2-iimpi-2022a
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help2man produces simple manual pages from the '--help' and '--version' output of other commands.

Available Modules

module load help2man/1.47.8-GCCcore-7.4.0

Warning

Warning: help2man/1.47.8-GCCcore-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.

Available Modules

module load hifiasm/0.19.7-GCC-11.3.0
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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-gimkl-2020a
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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-9.2.0
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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 HMMER2/2.3.2-GCC-9.2.0
Links

Available Modules

module load hooks/post-update.sample
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Pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

Available Modules

module load HOPS/0.33

Warning

Warning: HOPS/0.33 is old and marked for deletion. If you still need it, then please let us know.

Links

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.

Available Modules

module load HpcGridRunner/20181005
Links

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Available Modules

module load HTSeq/0.13.5-gimkl-2020a-Python-3.9.5
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A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

Available Modules

module load HTSlib/1.12-GCCcore-9.2.0
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Pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.

Available Modules

module load Humann/3.0.0.alpha.3
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Spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.

Available Modules

module load hunspell/1.7.0

Warning

Warning: hunspell/1.7.0 is old and marked for deletion. If you still need it, then please let us know.

Links

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

module load hwloc/1.11.13
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Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment.

Available Modules

module load HybPiper/2.0.1rc-Miniconda3
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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

module load hypothesis/6.68.2-gimkl-2022a-Python-3.10.5

Warning

Warning: hypothesis/6.68.2-gimkl-2022a-Python-3.10.5 is old and marked for deletion. If you still need it, then please let us know.

Links

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

module load Hypre/2.21.0-gimkl-2022a
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Intel C and C++ compilers

Available Modules

module load icc/2018.1.163-GCC-7.4.0
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Intel C, C++ & Fortran compilers

Available Modules

module load iccifort/2020.0.166
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C/C++ and Java libraries providing Unicode and Globalization support for software applications.

Available Modules

module load ICU/50.2-GCCcore-9.2.0
Links

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Available Modules

module load IDBA-UD/1.1.3-GCC-11.3.0
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Intel Fortran compiler

Available Modules

module load ifort/2018.1.163-GCC-7.4.0
Links

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

Available Modules

module load IGV/2.5.0
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Intel C/C++ and Fortran compilers, alongside Intel MPI.

Available Modules

module load iimpi/2018b

Warning

Links

Create, edit, compose, or convert bitmap images

Available Modules

module load ImageMagick/7.0.9-5-GCCcore-9.2.0
Links

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/2018.1.163-iimpi-2018b
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FFTW interfaces using Intel oneAPI Math Kernel Library

Available Modules

module load imkl-FFTW/2022.0.2-gimpi-2022a
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A lightweight JIT compiler for flexible data access in simulation applications

Available Modules

module load impalajit/20211029-foss-2023a
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The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. - Homepage: http://software.intel.com/en-us/intel-mpi-library/

Available Modules

module load impi/2017.6.256-iccifort-2017.6.256-GCC-5.4.0
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Genotype imputation and haplotype phasing.

Available Modules

module load IMPUTE/2.3.2
Links

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

Available Modules

module load info/exclude
Links

Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications

Available Modules

module load Inspector/2019_update5
Links

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.

Available Modules

module load intel/2018b
Links

Intel C, C++ & Fortran compilers (classic and oneAPI)

Available Modules

module load intel-compilers/2022.0.2
Links

Sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.

Available Modules

module load InterProScan/5.62-94.0-gimkl-2022aPerl-5.34.1-Python-3.11.3
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