title: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.
abstract: 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 presentSNP-siteswhich 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 (1842 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-sitesis implemented in C and is available under the open source license GNU GPL version 3.
authors.affiliation: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Page
authors.affiliation: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Taylor
authors.affiliation: 2 Computing, Engineering and Mathematics, University of Brighton, Moulsecoomb, Brighton, BN2 4GJ, UK.
authors.forename: Aidan J
authors.initials: AJ
authors.lastname: Delaney
authors.affiliation: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Jorge
authors.initials: J
authors.lastname: Soares
authors.affiliation: 3 Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Jacqueline A
authors.initials: JA
authors.lastname: Keane
authors.affiliation: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016678:Genome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: SNP calling; high throughput; software