shigeifinder
Link to section 'Introduction' of '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
Link to section 'Versions' of 'shigeifinder' Versions
- 1.3.2
Link to section 'Commands' of 'shigeifinder' Commands
- shigeifinder
Link to section 'Module' of 'shigeifinder' Module
You can load the modules by:
module load biocontainers
module load shigeifinder
Link to section 'Example job' of 'shigeifinder' 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 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