SNP-sites extracts single nucleotide polymorphisms (SNPs) from a multi-FASTA alignment outputs results in multiple formats for downstream analysis.

References:

• SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), 2016.

• SNP-sites Main Site

• Module Name: snp-sites (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load snp-sites
[+] Loading singularity  3.4.2  on cn3103 
[+] Loading snp-sites 2.4.1  ... 

[user@cn3144 ~]$ cd /data/user/SNP-SITES_TEST

[user@cn3144 ~]$ snp-sites PMEN1.aln.gz > PMEN1.out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. snp-sites.sh). For example:

#!/bin/bash
set -e
module load snp-sites
snp-sites /data/user/SNP-SITES_TEST/PMEN1.aln.gz > /data/user/SNP-SITES_TEST/PMEN1.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh

Create a swarmfile (e.g. snp-sites.swarm). For example:

snp-sites /data/user/SNP-SITES_TEST/PMEN1.aln.gz > /data/user/SNP-SITES_TEST/PMEN1.out
snp-sites /data/user/SNP-SITES_TEST/ST239.aln.gz > /data/user/SNP-SITES_TEST/ST239.out

Submit this job using the swarm command.

swarm -f snp-sites.swarm [-g #] [-t #] --module snp-sites