Software: Fraggenescan
Description
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.
Available Versions
| Unspecified: | 1.31 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/fraggenescan and its home page on Github.
Commands
- FragGeneScan
- run_FragGeneScan.pl
Module
You can load the modules by:
module load biocontainers
module load fraggenescan
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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