Difference between revisions of "SNAP"
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(Created page with "Category:SoftwareCategory:biologyCategory:bioinformaticsCategory:sequencing {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|snap}} |{{#vardefine:url|http://...") |
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| − | [[Category:Software]][[Category:biology | + | [[Category:Software]][[Category:biology]][[Category:sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|snap}} | |{{#vardefine:app|snap}} | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | SNAP is a | + | 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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<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | 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 |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_SNAP_DOC - documentation directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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. | + | [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 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: