: Rapid Efficient Extraction of SNPs from Multi-FASTA Alignments

Overview

Journal Microb Genom

Specialties Genetics
Microbiology

Date 2017 Mar 29

PMID 28348851

Citations 680

Authors

Andrew J Page

Ben Taylor

Aidan J Delaney

Jorge Soares

Torsten Seemann

Jacqueline A Keane

Simon R Harris

Affiliations

Soon will be listed here.

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

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References

Thompson J, Gibson T, Higgins D . Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2008; Chapter 2:Unit 2.3. DOI: 10.1002/0471250953.bi0203s00. View

Capella-Gutierrez S, Silla-Martinez J, Gabaldon T . trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009; 25(15):1972-3. PMC: 2712344. DOI: 10.1093/bioinformatics/btp348. View

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Lischer H, Excoffier L . PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics. 2011; 28(2):298-9. DOI: 10.1093/bioinformatics/btr642. View

Chewapreecha C, Harris S, Croucher N, Turner C, Marttinen P, Cheng L . Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014; 46(3):305-309. PMC: 3970364. DOI: 10.1038/ng.2895. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

Chang C, Chow C, Tellier L, Vattikuti S, Purcell S, Lee J . Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4:7. PMC: 4342193. DOI: 10.1186/s13742-015-0047-8. View

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

10.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

11.

Wong V, Baker S, Pickard D, Parkhill J, Page A, Feasey N . Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet. 2015; 47(6):632-9. PMC: 4921243. DOI: 10.1038/ng.3281. View

12.

Loytynoja A . Phylogeny-aware alignment with PRANK. Methods Mol Biol. 2013; 1079:155-70. DOI: 10.1007/978-1-62703-646-7_10. View

13.

Sudmant P, Rausch T, Gardner E, Handsaker R, Abyzov A, Huddleston J . An integrated map of structural variation in 2,504 human genomes. Nature. 2015; 526(7571):75-81. PMC: 4617611. DOI: 10.1038/nature15394. View

14.

Nasser W, Beres S, Olsen R, Dean M, Rice K, Long S . Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences. Proc Natl Acad Sci U S A. 2014; 111(17):E1768-76. PMC: 4035937. DOI: 10.1073/pnas.1403138111. View