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

doi:10.1093/bioinformatics/bts557

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 journal › Comment/debate › peer-review

8 Citations (Scopus)

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 language	English
Pages (from-to)	2983-2985
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	22
DOIs	https://doi.org/10.1093/bioinformatics/bts557
Publication status	Published - Nov 2012
Externally published	Yes

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title = "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.",

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T2 - A variation browsing and analysis tool for variants derived from next-generation sequencing data

AU - Preston, Mark D.

AU - Manske, Magnus

AU - Horner, Neil

AU - Assefa, Samuel

AU - Campino, Susana

AU - Auburn, Sarah

AU - Zongo, Issaka

AU - Ouedraogo, Jean Bosco

AU - Nosten, Francois

AU - Anderson, Tim

AU - Clark, Taane G.

PY - 2012/11

Y1 - 2012/11

N2 - 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.

AB - 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.

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M3 - Comment/debate

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SN - 1367-4803

VL - 28

SP - 2983

EP - 2985

JO - Bioinformatics

JF - Bioinformatics

IS - 22

ER -

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

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