View source for Stacks

[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|stacks}}
|{{#vardefine:url|http://creskolab.uoregon.edu/stacks/}}
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|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
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|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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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.

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{{#if: {{#var: mod}}|==Execution Environment and Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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{{#if: {{#var: exe}}|==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.
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
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{{#if: {{#var: testing}}|==Performance==
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{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
DOUBLE_CLICK_TO_WRITE_CITATION_HERE
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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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