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 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.
Highlights
As the cost of sequencing has rapidly decreased, the number of samples sequenced within a study has proportionately increased and stands in the thousands (Chewapreecha et al, 2014; Nasser et al, 2014; Wong et al, 2015)
A common task in prokaryotic bioinformatics analysis is the extraction of all single nucleotide polymorphisms (SNPs) from a multiple FASTA alignment
Whilst it is a simple problem to describe, current tools cannot rapidly or efficiently extract SNPs in the increasingly large datasets found in prokaryotic population studies
Summary
Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is 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. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3. 1. The source code for SNP-sites is available from GitHub under GNU GPL v3; (URL – https://github.com/sangerpathogens/snp-sites) 2.
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