Stacks

Introduction

Stacks is a software pipeline for building loci from RAD-seq.

For more information, please check its website: https://biocontainers.pro/tools/stacks and its home page: https://catchenlab.life.illinois.edu/stacks/.

Versions

• 2.60

Commands

• clone_filter

• count_fixed_catalog_snps.py

• cstacks

• denovo_map.pl

• gstacks

• integrate_alignments.py

• kmer_filter

• phasedstacks

• populations

• process_radtags

• process_shortreads

• ref_map.pl

• sstacks

• stacks-dist-extract

• stacks-gdb

• stacks-integrate-alignments

• tsv2bam

• ustacks

Module

You can load the modules by:

module load biocontainers
module load stacks

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Stacks on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=stacks
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers stacks

denovo_map.pl -T 8 -M 4 -o ./stacks/  \
    --samples ./samples --popmap ./popmaps/popmap