Show simple item record

dc.contributor.authorNaeem, Raeece
dc.contributor.authorHidayah, Lailatul
dc.contributor.authorPreston, Mark D.
dc.contributor.authorClark, Taane G.
dc.contributor.authorPain, Arnab
dc.date.accessioned2014-11-11T14:28:00Z
dc.date.available2014-11-11T14:28:00Z
dc.date.issued2014-04-03
dc.identifier.citationNaeem R, Hidayah L, Preston MD, Clark TG, Pain A (2014) SVAMP: sequence variation analysis, maps and phylogeny. Bioinformatics 30: 2227-2229. doi:10.1093/bioinformatics/btu176.
dc.identifier.issn13674803
dc.identifier.pmid24700318
dc.identifier.doi10.1093/bioinformatics/btu176
dc.identifier.urihttp://hdl.handle.net/10754/334516
dc.description.abstractSummary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima's D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. Availability and implementation: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp. © The Author 2014.
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/
dc.titleSVAMP: Sequence variation analysis, maps and phylogeny
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalBioinformatics
dc.identifier.pmcidPMC4103593
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personNaeem, Raeece
kaust.personHidayah, Lailatul
kaust.personPain, Arnab
refterms.dateFOA2018-06-13T15:40:48Z
dc.date.published-online2014-04-03
dc.date.published-print2014-08-01


Files in this item

Thumbnail
Name:
Article-Bioinforma-SVAMP_Sequ-2014.pdf
Size:
164.8Kb
Format:
PDF
Description:
Article - Full Text
Thumbnail
Name:
Supplement_1_-_Bioinforma-SVAMP_Sequ-2014.docx
Size:
2.157Mb
Format:
Microsoft Word 2007
Description:
Supplemental File 1

This item appears in the following Collection(s)

Show simple item record

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.