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

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 effici...

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Bibliographic Details
Published in:Microbial genomics Vol. 2; no. 4; p. e000056
Main Authors: Page, Andrew J., Taylor, Ben, Delaney, Aidan J., Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A., Harris, Simon R.
Format: Journal Article
Language:English
Published: England Microbiology Society 01.04.2016
Subjects:
Algorithms
Base Sequence
Genome - genetics
High-Throughput Nucleotide Sequencing
Methods Paper
Polymorphism, Single Nucleotide - genetics
Sequence Alignment
Sequence Analysis, DNA - methods
Software
software
high throughput
SNP calling
ISSN:2057-5858, 2057-5858
Online Access:Get full text
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Summary: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.
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All supporting data, code and protocols have been provided within the article or through supplementary data files.
ISSN:2057-5858
2057-5858
DOI:10.1099/mgen.0.000056