Snp-sites
Introduction
SNP-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment.
For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/snp-sites
Versions
2.5.1
Commands
snp-sites
Module
You can load the modules by:
module load biocontainers
module load snp-sites
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-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