Shigeifinder

Introduction

Shigeifinder is a tool that is used to identify differentiate Shigella/EIEC using cluster-specific genes and identify the serotype using O-antigen/H-antigen genes. For more information, please check: Docker hub: https://hub.docker.com/r/staphb/shigeifinder Home page: https://github.com/LanLab/ShigEiFinder

Versions

  • 1.3.2

Commands

  • shigeifinder

Module

You can load the modules by:

module load biocontainers
module load shigeifinder

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 shigeifinder on our clusters:

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

module --force purge
ml biocontainers shigeifinder