Difference between revisions of "Stacks"
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Moskalenko (talk | contribs) m (Text replace - "<!--Run-->" to "==System Variables== * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory <!--Run--> ") |
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|{{#vardefine:url|http://creskolab.uoregon.edu/stacks/}} | |{{#vardefine:url|http://creskolab.uoregon.edu/stacks/}} | ||
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|{{#vardefine:exe|1}} <!--RUNNING --> | |{{#vardefine:exe|1}} <!--RUNNING --> | ||
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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. | 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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==Required Modules== | ==Required Modules== | ||
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*{{#var:app}} | *{{#var:app}} | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
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The command line pipeline is available via the "stacks" module. | The command line pipeline is available via the "stacks" module. | ||
Revision as of 19:56, 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.
Required Modules
Serial
- stacks
System Variables
- HPC_{{#uppercase:stacks}}_DIR - installation directory
Additional Information
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.