fraggenescan
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'fraggenescan' Versions
- 1.31
Link to section 'Commands' of 'fraggenescan' Commands
- FragGeneScan
- run_FragGeneScan.pl
Link to section 'Module' of 'fraggenescan' Module
You can load the modules by:
module load biocontainers
module load fraggenescan
Link to section 'Example job' of 'fraggenescan' Example job
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