Difference between revisions of "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. | ||
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Revision as of 02:41, 10 August 2012
Description
FragGeneScan is an application for finding (fragmented) genes in short reads.
Execution Environment and Modules
To use fraggenescan with the environment modules system at HPC the following commands are available:
Get module information for fraggenescan:
$module spider fraggenescan
Load the default application module:
$module load fraggenescan
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_FRAGGENESCAN_DIR - directory where fraggenescan is located.
- HPC_FRAGGENESCAN_BIN - executable directory.
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