Difference between revisions of "AMPtk"
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(Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|amptk}} |{{#vardefine:url|https://githu...") |
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==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - binary directory | ||
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory | * HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory | ||
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 14:11, 20 January 2017
Description
AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.
Required Modules
Serial
- gcc/5.2.0
- amptk
System Variables
- HPC_{{#uppercase:amptk}}_DIR - installation directory
- HPC_{{#uppercase:amptk}}_BIN - binary directory
- HPC_{{#uppercase:amptk}}_DOC - documentation directory