SVAMP: Sequence variation analysis, maps and phylogeny

Handle URI:
http://hdl.handle.net/10754/334516
Title:
SVAMP: Sequence variation analysis, maps and phylogeny
Authors:
Naeem, Raeece ( 0000-0003-1734-1007 ) ; Hidayah, Lailatul; Preston, Mark D.; Clark, Taane G.; Pain, Arnab ( 0000-0002-1755-2819 )
Abstract:
Summary: 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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Pathogen Genomics Laboratory
Citation:
Naeem 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.
Publisher:
Oxford University Press
Journal:
Bioinformatics
Issue Date:
3-Apr-2014
DOI:
10.1093/bioinformatics/btu176
PubMed ID:
24700318
PubMed Central ID:
PMC4103593
Type:
Article
ISSN:
13674803
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorNaeem, Raeeceen
dc.contributor.authorHidayah, Lailatulen
dc.contributor.authorPreston, Mark D.en
dc.contributor.authorClark, Taane G.en
dc.contributor.authorPain, Arnaben
dc.date.accessioned2014-11-11T14:28:00Z-
dc.date.available2014-11-11T14:28:00Z-
dc.date.issued2014-04-03en
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.en
dc.identifier.issn13674803en
dc.identifier.pmid24700318en
dc.identifier.doi10.1093/bioinformatics/btu176en
dc.identifier.urihttp://hdl.handle.net/10754/334516en
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.en
dc.language.isoenen
dc.publisherOxford University Pressen
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.en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.titleSVAMP: Sequence variation analysis, maps and phylogenyen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC4103593en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorNaeem, Raeeceen
kaust.authorHidayah, Lailatulen
kaust.authorPain, Arnaben

Related articles on PubMed

This item is licensed under a Creative Commons License
Creative Commons
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.