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Fraggenescan

Introduction ~~~~~~~~ Fraggenescan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

For more information, please check its website: https://biocontainers.pro/tools/fraggenescan and its home page on Github.

Versions

  • 1.31

Commands ~~~~~~~ - FragGeneScan - run_FragGeneScan.pl

Module

You can load the modules by:

module load biocontainers
module load fraggenescan

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Fraggenescan on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fraggenescan
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers fraggenescan

FragGeneScanRs -t 454_10 < example/NC_000913-454.fna > example/NC_000913-454.faa