Stacks

Introduction

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Installed version

The currently installed version of Stacks is 1.42.

Using Stacks on the HPC cluster

If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. You can do that by using the command

module load Stacks

Since there is only one version of Stacks installed, you dont need to specify a version.

Documentation

A manual for Stacks can be found here here.