platon
Link to section 'Introduction' of 'platon' Introduction
Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.
BioContainers: https://biocontainers.pro/tools/platon
Home page: https://github.com/oschwengers/platon
Link to section 'Versions' of 'platon' Versions
- 1.6
Link to section 'Commands' of 'platon' Commands
- platon
Link to section 'Module' of 'platon' Module
You can load the modules by:
module load biocontainers
module load platon
The environment variable PLATON_DB is set as /depot/itap/datasets/platon/db. This directory contains the required database.
Link to section 'Example job' of 'platon' 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 platon on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=platon
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers platon
platon --verbose --threads 4 contigs.fasta