Stacks

Introduction

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

For more information, please check:
BioContainers: https://biocontainers.pro/tools/stacks
Home page: https://catchenlab.life.illinois.edu/stacks/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.60, 2.64, 2.68

BELL

2.60, 2.68

GAUTSCHI

2.60

NEGISHI

2.60, 2.64, 2.68

SCHOLAR

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 -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers stacks

# Your stacks workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers stacks

# Your stacks workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers stacks

# Your stacks workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers stacks

# Your stacks workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers stacks

# Your stacks workflow...