Difference between revisions of "Subread"

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(Created page with "Category:SoftwareCategory:BiologyCategory:SequencingCategory:SNP {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|subread}} |{{#vardefine:url|http://bioinf.w...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:SNP]]
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[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Variant Calling]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|subread}}
 
|{{#vardefine:app|subread}}
|{{#vardefine:url|http://bioinf.wehi.edu.au/subread-package/}}
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|{{#vardefine:url|http://subread.sourceforge.net/}}
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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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===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 12:57, 15 August 2022

Description

subread website  

The Subread package: a tool kit for processing next-gen sequencing data

Environment Modules

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

System Variables

  • HPC_SUBREAD_DIR - installation directory




Citation

If you publish research that uses subread you have to cite it as follows:

If you use the Subread or Subjunc aligners, please cite: Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108

If you use the featureCounts program, please cite: Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30