Subread: Difference between revisions
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[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category: | [[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Variant Calling]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|subread}} | |{{#vardefine:app|subread}} | ||
|{{#vardefine:url|http:// | |{{#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--> | ||
== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
< | |||
==System Variables== | ==System Variables== | ||
* HPC_{{ | * 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
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