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Microb Genom. 2016 Apr 29;2(4):e000056. doi: 10.1099/mgen.0.000056. eCollection 2016 Apr.

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

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1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
2 Computing, Engineering and Mathematics, University of Brighton, Moulsecoomb, Brighton, BN2 4GJ, UK.
3 Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, Australia.


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 (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-sites is implemented in C and is available under the open source license GNU GPL version 3.


SNP calling; high throughput; software

[Indexed for MEDLINE]
Free PMC Article

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