Difference between revisions of "Stampy"

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[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Sequencing]]
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[[Category:Software]][[Category:Biology]][[Category:Sequencing]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|stampy}}
 
|{{#vardefine:app|stampy}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* gcc/5.2.0
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory

Latest revision as of 20:45, 12 August 2022

Description

stampy website  

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model.

Environment Modules

Run module spider stampy to find out what environment modules are available for this application.

System Variables

  • HPC_STAMPY_DIR - installation directory
  • HPC_STAMPY_BIN - executable directory