Dataset Information

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

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.The C++-based software VarB and user manual are available from www.pathogenseq.org/varb.taane.clark@lshtm.ac.uk

SUBMITTER: Preston MD

PROVIDER: S-EPMC3496337 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature

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

Preston Mark D MD Manske Magnus M Horner Neil N Assefa Samuel S Campino Susana S Auburn Sarah S Zongo Issaka I Ouedraogo Jean-Bosco JB Nosten Francois F Anderson Tim T Clark Taane G TG

Bioinformatics (Oxford, England) 20120913 22

<h4>Summary</h4>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 ...[more]

PMID: 22976080

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Dataset Information

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

Publications

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

Similar Datasets

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