Difference between revisions of "Stacks"
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Revision as of 16:33, 10 August 2012
Description
Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
Execution Environment and Modules
To use stacks with the environment modules system at HPC the following commands are available:
Get module information for stacks:
$module spider stacks
Load the default application module:
$module load stacks
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_STACKS_DIR - directory where stacks is located.
How To Run
The command line pipeline is available via the "stacks" module.
The web interface that can be used for visualizing genetic maps and correcting the analysis is not installed, but is being evaluated for installation.