plasmidfinder
Link to section 'Introduction' of 'plasmidfinder' Introduction
PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.
Docker hub: https://hub.docker.com/r/staphb/plasmidfinder
Home page: https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
Link to section 'Versions' of 'plasmidfinder' Versions
- 2.1.6
Link to section 'Commands' of 'plasmidfinder' Commands
- plasmidfinder.py
Link to section 'Module' of 'plasmidfinder' Module
You can load the modules by:
module load biocontainers
module load plasmidfinder
Link to section 'Example job' of 'plasmidfinder' 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 plasmidfinder on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=plasmidfinder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers plasmidfinder
plasmidfinder.py -p test/database \
-i test/test.fsa -o output -mp blastn -x -q