Snp-dists

Introduction

Snp-dists is a tool to convert a FASTA alignment to SNP distance matrix.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/snp-dists

Home page: https://github.com/tseemann/snp-dists

Versions

• 0.8.2

Commands

• snp-dists

Module

You can load the modules by:

module load biocontainers
module load snp-dists

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 snp-dists on our clusters:

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

module --force purge
ml biocontainers snp-dists

snp-dists test/good.aln > distances.tab