Jan 29, 2016

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

BioRxiv : the Preprint Server for Biology
Andrew PageSimon R Harris

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 (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.

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Mentioned in this Paper

Study
Genome
Genetic Analysis
Site
Extraction
R Programming Language
Genome Sequencing
Core
Single Nucleotide Polymorphism
Population Study (Research Activity)

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