Stacks

Overview

Stacks: 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.

Using

Use the module name stacks to discover versions available and to load the application.

Multicore

Some of the various stacks application commands allow you define multiple cores within their calls. Please see the commands help for more information. For example:

[]$ gstacks -h
gstacks 2.63
...
  -t,--threads: number of threads to use (default: 1)

[]$ denovo_map.pl
...
    -T, --threads: the number of threads/CPUs to use (default: 1).
 by using the application_name --flag options. See application_name --help for more information.