Difference between revisions of "SNAP"

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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 +
* HPC_SNAP_DOC - documentation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Revision as of 20:53, 27 May 2022

Description

snap website  

SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and determines where, how well and how unambiguously they match to a given reference genome. This is a computationally challenging problem because reference genomes are big (the human genome is over 3 billion base pairs long) and are often highly repetitive.

Environment Modules

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

System Variables

  • HPC_SNAP_DIR - installation directory
  • HPC_SNAP_BIN - executable directory
  • HPC_SNAP_DOC - documentation directory




Citation

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

Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011.

William J. Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, and David Patterson. BioRxiv, November 2021.