FragGeneScan

Description

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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