mlst
Link to section 'Introduction' of 'mlst' Introduction
Mlst is used to scan contig files against traditional PubMLST typing schemes.
Docker hub: https://hub.docker.com/r/staphb/mlst
Home page: https://github.com/tseemann/mlst
Link to section 'Versions' of 'mlst' Versions
- 2.22.0
- 2.23.0
Link to section 'Commands' of 'mlst' Commands
- mlst
Link to section 'Module' of 'mlst' Module
You can load the modules by:
module load biocontainers
module load mlst
Link to section 'Example job' of 'mlst' 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 mlst on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mlst
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers mlst
mlst contigs.fa
mlst genome.gbk.gz