VarB: A variation browsing and analysis tool for variants derived from next-generation sequencing data

Mark D. Preston, Magnus Manske, Neil Horner, Samuel Assefa, Susana Campino, Sarah Auburn, Issaka Zongo, Jean Bosco Ouedraogo, Francois Nosten, Tim Anderson, Taane G. Clark

    Research output: Contribution to journalArticle

    8 Scopus citations

    Abstract

    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.

    Original languageEnglish (US)
    Pages (from-to)2983-2985
    Number of pages3
    JournalBioinformatics
    Volume28
    Issue number22
    DOIs
    Publication statusPublished - Nov 1 2012

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    ASJC Scopus subject areas

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

    Cite this

    Preston, M. D., Manske, M., Horner, N., Assefa, S., Campino, S., Auburn, S., ... Clark, T. G. (2012). VarB: A variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics, 28(22), 2983-2985. https://doi.org/10.1093/bioinformatics/bts557