Gamma

Introduction

GAMMA (Gene Allele Mutation Microbial Assessment) is a command line tool that finds gene matches in microbial genomic data using protein coding (rather than nucleotide) identity, and then translates and annotates the match by providing the type (i.e., mutant, truncation, etc.) and a translated description (i.e., Y190S mutant, truncation at residue 110, etc.). Because microbial gene families often have multiple alleles and existing databases are rarely exhaustive, GAMMA is helpful in both identifying and explaining how unique alleles differ from their closest known matches.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/gamma
Home page: https://github.com/rastanton/GAMMA

Versions

  • 1.4

  • 2.2

Commands

  • GAMMA-S.py

  • GAMMA.py

Module

You can load the modules by:

module load biocontainers
module load gamma

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 gamma on our clusters:

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

module --force purge
ml biocontainers gamma

GAMMA.py DHQP1701672_complete_genome.fasta ResFinderDB_Combined_05-06-20.fsa GAMMA_Test