SVAMP: sequence variation analysis, maps and phylogeny.


Naeem, R; Hidayah, L; Preston, MD; Clark, TG; Pain, A; (2014) SVAMP: sequence variation analysis, maps and phylogeny. Bioinformatics (Oxford, England), 30 (15). pp. 2227-9. ISSN 1367-4803 DOI: 10.1093/bioinformatics/btu176

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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.<br/> AVAILABILITY AND IMPLEMENTATION: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp<br/> CONTACT: arnab.pain@kaust.edu.sa or arnab.pain@cantab.net<br/> SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.<br/>

Item Type: Article
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Research Centre: Centre for Statistical Methodology
PubMed ID: 24700318
Web of Science ID: 340049100025
URI: http://researchonline.lshtm.ac.uk/id/eprint/1673630

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