Difference between revisions of "SNAP"

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[[Category:Software]][[Category:biology]][[Category:bioinformatics]][[Category:sequencing]]
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[[Category:Software]][[Category:biology]][[Category:sequencing]]
 
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|{{#vardefine:app|snap}}
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
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SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
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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.
 
 
 
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==Environment Modules==
 
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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* HPC_SNAP_DOC - documentation directory
 
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} 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.
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[https://arxiv.org/abs/1111.5572 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.]
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[https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1  William J. Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, and David Patterson.  BioRxiv, November 2021.]
  
 
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Latest revision as of 20:42, 12 August 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.