RT Journal Article
SR Electronic
T1 SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 038190
DO 10.1101/038190
A1 Andrew J. Page
A1 Ben Taylor
A1 Aidan J. Delaney
A1 Jorge Soares
A1 Torsten Seemann
A1 Jacqueline A. Keane
A1 Simon R. Harris
YR 2016
UL http://biorxiv.org/content/early/2016/01/29/038190.abstract
AB Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. 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. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.SNPsingle nucleotide polymorphismVCFVariant Call Format