Introduction

There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats. We have developed VarB software that can be used to visualize variant call format files in real time, as well as identify regions under balancing selection and informative markers to differentiate user-defined groups (e.g. populations). We demonstrate its utility using sequence data from 50 Plasmodium falciparum isolates comprising two different continents and confirm known signals from genomic regions that contain important antigenic and anti-malarial drug-resistance genes.The C++-based software VarB and user manual are available from www.pathogenseq.org/varb.taane.clark@lshtm.ac.uk

Publications

  1. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.
    Cite this
    Preston MD, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo JB, Nosten F, Anderson T, Clark TG, 2012-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Mark D Preston
    Developer

    Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine

  2. Magnus Manske
    Developer

  3. Neil Horner
    Developer

  4. Samuel Assefa
    Developer

  5. Susana Campino
    Developer

  6. Sarah Auburn
    Developer

  7. Issaka Zongo
    Developer

  8. Jean-Bosco Ouedraogo
    Developer

  9. Francois Nosten
    Developer

  10. Tim Anderson
    Developer

  11. Taane G Clark
    Investigator

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Summary
AccessionBT000780
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByTaane G Clark