SVAMP: sequence variation analysis, maps and phylogeny.
Where this comes from
- Record sourced from PubMed, PMID 24700318.
- Also identified by DOI 10.1093/bioinformatics/btu176 and PMC identifier 4103593.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp arnab.pain@kaust.edu.sa or arnab.pain@cantab.net Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genetic Variation
- Genomics
- Phylogeny
- Software