SVAMP: sequence variation analysis, maps and phylogeny.
CONCLUSIONS
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.


METHODS
The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp


BACKGROUND
arnab.pain@kaust.edu.sa or arnab.pain@cantab.net


BACKGROUND
Supplementary data are available at Bioinformatics online.
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Raeece
R
Naeem
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Lailatul
L
Hidayah
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Mark D
MD
Preston
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Taane G
TG
Clark
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Arnab
A
Pain
D004196:Disease Outbreaks; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016778:Malaria, Falciparum / Q000453:epidemiology; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics / Q000502:physiology; D010802:Phylogeny; D010963:Plasmodium falciparum / Q000235:genetics / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D012984:Software; D013203:Staphylococcal Infections / Q000453:epidemiology; D013997:Time Factors