SVAMP: sequence variation analysis, maps and phylogeny.

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

CONTACT:

[email protected] or [email protected]

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

• Authors: Raeece Naeem, Lailatul Hidayah, Mark D Preston, Taane G Clark, Arnab Pain
• Journal: Bioinformatics (Oxford, England) (Bioinformatics) Vol. 30 Issue 15 Pg. 2227-9 (Aug 01 2014) ISSN: 1367-4811 [Electronic] England
• PMID: 24700318 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author 2014. Published by Oxford University Press.

Topics

• Disease Outbreaks
• Genetic Variation
• Genomics (methods)
• High-Throughput Nucleotide Sequencing
• Humans
• Malaria, Falciparum (epidemiology)
• Methicillin-Resistant Staphylococcus aureus (genetics, physiology)
• Phylogeny
• Plasmodium falciparum (genetics, physiology)
• Polymorphism, Single Nucleotide
• Software
• Staphylococcal Infections (epidemiology)
• Time Factors