ipyrad

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.

ipyrad Homepage

Available Modules¶

Mahuika

module load ipyrad/0.9.85-gimkl-2022a-Python-3.10.5

Description¶

ipyrad, an interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types. Please explore the documentation to find out more about the features of ipyrad.\

Home page is at https://ipyrad.readthedocs.io/en/latest/index.html

Cite the Manuscript¶

Eaton DAR & Overcast I. "ipyrad: Interactive assembly and analysis of RADseq datasets." Bioinformatics (2020).

License¶

GPLv3

Getting Started¶

Following example uses rad_example which can be downloaded as per instructions on https://ipyrad.readthedocs.io/en/latest/tutorial_advanced_cli.html

curl -LkO https://eaton-lab.org/data/ipsimdata.tar.gz
tar -xvzf ipsimdata.tar.gz

Start by creating a new Assembly data1 , and then we’ll edit the params file to tell it how to find the input data files for this data set.

module purge
module load ipyrad/0.9.85-gimkl-2022a-Python-3.10.5
ipyrad -n data1

New file 'params-data1.txt' created in ........

params-data1.txt will be created on current working directory. Review and edit the paths in parameter file to match the destinations of input data, barcode paths,etc.

Slurm Script for Using Multiple CPUs a Single Compute Node¶

#!/bin/bash

#SBATCH --account       nesi12345
#SBATCH --job-name      ipyrad
#SBATCH --cpus-per-task 12
#SBATCH --time          00:05:00
#SBATCH --mem           10G
#SBATCH --output        ipyrad_output_%j.txt

## assembly name
assembly_name="data1"

## load environment and module
module purge
module load ipyrad/0.9.85-gimkl-2022a-Python-3.10.5

## create, prepare and change to a job specific dir
jobdir="ipyrad_${SLURM_JOB_ID}"
params="params-${assembly_name}.txt"

mkdir $jobdir
sed "s#$(pwd) #$(pwd)/$jobdir#" $params > $jobdir/$params
cd $jobdir


## call ipyrad on your params file and perform 7 steps from the workflow
srun ipyrad -p $params -s 12 --force