SVAMP: Sequence variation analysis, maps and phylogeny

Raeece Naeem, Lailatul Hidayah, Mark D. Preston, Taane G. Clark, Arnab Pain

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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.
Original languageEnglish (US)
Pages (from-to)2227-2229
Number of pages3
JournalBioinformatics
Volume30
Issue number15
DOIs
StatePublished - Apr 3 2014

ASJC Scopus subject areas

  • Biochemistry
  • Computational Theory and Mathematics
  • Computational Mathematics
  • Molecular Biology
  • Statistics and Probability
  • Computer Science Applications

Fingerprint Dive into the research topics of 'SVAMP: Sequence variation analysis, maps and phylogeny'. Together they form a unique fingerprint.

Cite this