Stacks

Overview

Stacks is a software pipeline used to build loci from short-read genetic sequences. It can use restriction enzyme-based data for building genetic maps and performing population phylogeography and genomics

Availability

Cluster	Module/Version
BOSE	Not Available
BGSC	stacks/2.57

Note: You can simply use module load stacks to activate the most recently installed version of this software.

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load stacks    # Load Stacks
sstacks -P my-stacks-files/ -M ./my-popmap-file

Real Example

Has your research group used Stacks in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include one (or both) of the following citations in your papers to support continued development of Stacks.

J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.

J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.