srst2
Link to section 'Introduction' of 'srst2' Introduction
Srst2 is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/srst2
Home page: https://github.com/katholt/srst2
Link to section 'Versions' of 'srst2' Versions
- 0.2.0
Link to section 'Commands' of 'srst2' Commands
- getmlst.py
- srst2
- slurm_srst2.py
Link to section 'Module' of 'srst2' Module
You can load the modules by:
module load biocontainers
module load srst2
Link to section 'Example job' of 'srst2' 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 srst2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=srst2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers srst2