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 journalComment/debate

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
Pages (from-to)2983-2985
Number of pages3
JournalBioinformatics
Volume28
Issue number22
DOIs
Publication statusPublished - Nov 2012
Externally publishedYes

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    Preston, M. D., Manske, M., Horner, N., Assefa, S., Campino, S., Auburn, S., Zongo, I., Ouedraogo, J. B., Nosten, F., Anderson, T., & 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