Parsnp

Introduction

Parsnp is used to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours.

For more information, please check its website: https://biocontainers.pro/tools/parsnp and its home page on Github.

Versions

• 1.6.2

Commands

• parsnp

Module

You can load the modules by:

module load biocontainers
module load parsnp

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 Parsnp on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=parsnp
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers parsnp

parsnp -g examples/mers_virus/ref/England1.gbk \
     -d examples/mers_virus/genomes/*.fna -c -p 8