Platon

Introduction

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/platon

Home page: https://github.com/oschwengers/platon

Versions

• 1.6

Commands

• platon

Module

You can load the modules by:

module load biocontainers
module load platon

Note

The environment variable PLATON_DB is set as /depot/itap/datasets/platon/db. This directory contains the required database.

Example job

Warning

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