Software: Parsnp
Description
Parsnp is used to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours.
Available Versions
| Unspecified: | 1.6.2 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/parsnp and its home page on Github.
Commands
- parsnp
Module
You can load the modules by:
module load biocontainers
module load parsnp
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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