Software: SNP-sites
Description
SNP-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment.
Available Versions
| Unspecified: | 2.5.1 |
|---|
Docker hub: https://hub.docker.com/r/staphb/snp-sites
Home page: https://github.com/sanger-pathogens/snp-sites
Commands
- snp-sites
Module
You can load the modules by:
module load biocontainers
module load snp-sites
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 snp-sites 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-sites
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snp-sites
snp-sites salmonella_serovars_core_genes.aln