We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
- HPC_SNP-SITES_DIR - installation directory
If you publish research that uses snp-sites you have to cite it as follows:
Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", bioRxiv, doi: http://dx.doi.org/10.1101/038190 (2016).