When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes

PloS One
Shea N Gardner, Barry G Hall

Abstract

Effective use of rapid and inexpensive whole genome sequencing for microbes requires fast, memory efficient bioinformatics tools for sequence comparison. The kSNP v2 software finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation; better scaling for draft genomes available as assembled contigs or raw, unassembled reads; a tool to identify the optimal value of k; distribution of packages of executables for Linux and Mac OS X for ease of installation and user-friendly use; and a detailed User Guide. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a single reference genome. Most target sets with hundreds of genomes complete in minutes to hours. SNP phylogenies are built by maximum likelihood, parsimony, and distance, based on all SNPs, only core SNPs, or SNPs present in some intermediate user-specified fraction of targets. The SNP-based trees that result are consistent with known taxonomy. kSNP v2 can handle many gigabases of sequence in a single run, and if one or more annotated genomes are included in the target set, SNPs are annotated with protein coding and other information (UTRs, ...Continue Reading

References

Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Nov 24, 2007·BMC Bioinformatics·Daniel H HusonRegula Rupp
Jan 15, 2008·Molecular Biology and Evolution·Barry G Hall
Dec 17, 2009·PloS One·Bryan Kolaczkowski, Joseph W Thornton
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Aug 19, 2011·Journal of Clinical Microbiology·Stephen J Salipante, Barry G Hall
Feb 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Yonatan H GradWilliam P Hanage
Jul 12, 2012·Systematic Biology·Daniel H Huson, Celine Scornavacca
May 30, 2013·Journal of Virological Methods·Shea N Gardner, Crystal J Jaing

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Citations

Jan 17, 2016·Annual Review of Food Science and Technology·Xiangyu DengRene S Hendriksen
Dec 10, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Theresa J SmithLeonard A Smith
Aug 25, 2015·Cell Host & Microbe·Peter JorthPradeep K Singh
Jun 8, 2015·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Rebecca J DavisRaymond Chan
Sep 1, 2015·Genome Announcements·Michael R WeigandM Lucia Tondella
Apr 18, 2015·Genome Announcements·Marie BugarelGuy H Loneragan
Feb 25, 2015·Frontiers in Microbiology·Scott T ChanceyDavid S Stephens
Mar 5, 2015·PeerJ·Eduardo Castro-NallarKeith A Crandall
Mar 8, 2014·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Erin E EpsonWendy M Bamberg
Sep 21, 2016·Emerging Infectious Diseases·Cecilia B KretzUNKNOWN Niger Response Team
Oct 14, 2016·Frontiers in Cellular and Infection Microbiology·Pedro F Soler-LlorénsAnne Keriel
Nov 4, 2015·BMC Bioinformatics·Saulo Alves AflitosDick de Ridder
Aug 16, 2016·International Journal of Systematic and Evolutionary Microbiology·Rachel A MillerJasna Kovac
Nov 3, 2015·Scientific Reports·Nouri L Ben ZakourMark J Walker
May 21, 2014·The American Journal of Tropical Medicine and Hygiene·Daniel N WolfeKevin Carlton
Nov 28, 2016·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·S SchlebuschS J Van Hal
Jun 24, 2017·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Taichiro TakemuraTetsu Yamashiro
May 16, 2017·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Temitope A FolaranmiSarah A Meyer
Nov 19, 2014·Nucleic Acids Research·Raluca UricaruPierre Peterlongo
Feb 28, 2018·Antimicrobial Agents and Chemotherapy·Ryota GomiYasufumi Matsumura
Sep 26, 2017·International Journal of Systematic and Evolutionary Microbiology·Laura B GoodmanJasna Kovac
Sep 15, 2017·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Karen J LeCountMatthew M Erdman

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Software Mentioned

FastTreeMP
EvolveAGene3
fastq
FigTree
iMac
BopGenomes
MSTgold
seqtk
BLAST
MUMmer

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