Difference between revisions of "FragGeneScan"
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Revision as of 01:53, 10 August 2012
Description
FragGeneScan is an application for finding (fragmented) genes in short reads. Template:App Location
Available versions
- 1.16.
Running the application using 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