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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