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