SVAMP

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
CONTACT: arnab.pain@kaust.edu.sa or arnab.pain@cantab.net
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SVAMP: sequence variation analysis, maps and phylogeny.

SVAMP is a software application for analyzing genomic variants in the context of geographical metadata. It allows users to generate phylogenetic trees quickly, visualize allele frequency maps and geographical maps of isolates, and calculate Tajimas D metric, single nucleotide polymorphism density, GC, and variation density.

SVAMP

Topic

Detail

Publications

Download and documentation