Difference between revisions of "FragGeneScan"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|fraggenescan}} | |{{#vardefine:app|fraggenescan}} | ||
|{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}} | |{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}} | ||
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FragGeneScan is an application for finding (fragmented) genes in short reads. | FragGeneScan is an application for finding (fragmented) genes in short reads. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_FRAGGENESCAN_BIN - executable directory. | * HPC_FRAGGENESCAN_BIN - executable directory. | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary. | Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary. | ||
Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program. | Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program. | ||
| + | }} | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747] | Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747] | ||
|}} | |}} | ||
Latest revision as of 16:48, 15 August 2022
Description
FragGeneScan is an application for finding (fragmented) genes in short reads.
Environment Modules
Run module spider fraggenescan to find out what environment modules are available for this application.
System Variables
- HPC_FRAGGENESCAN_DIR - installation directory
- HPC_FRAGGENESCAN_BIN - executable directory.
Additional Information
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary.
Read the usage documentation for details on how to run the program.
Citation
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747