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 › Article › peer-review

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

ASJC Scopus subject areas

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

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10.1093/bioinformatics/bts557

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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.",

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

note = "Funding Information: 1Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, 2Malaria Programme, Wellcome Trust Sanger Institute (WTSI), Cambridge CB10 1SA, 3Faculty of Health, Cranfield University, Cranfield MK43 0AL, UK, 4Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso, Burkina Faso, 5Shoklo Malaria & Mahidol-Oxford Clinical Research Units, Mae Sot, Tak, Thailand and 6Texas Biomedical Research Institute, San Antonio, TX 78245, USA",

year = "2012",

month = nov,

doi = "10.1093/bioinformatics/bts557",

language = "English (US)",

volume = "28",

pages = "2983--2985",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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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.

N1 - Funding Information: 1Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, 2Malaria Programme, Wellcome Trust Sanger Institute (WTSI), Cambridge CB10 1SA, 3Faculty of Health, Cranfield University, Cranfield MK43 0AL, UK, 4Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso, Burkina Faso, 5Shoklo Malaria & Mahidol-Oxford Clinical Research Units, Mae Sot, Tak, Thailand and 6Texas Biomedical Research Institute, San Antonio, TX 78245, USA

PY - 2012/11

Y1 - 2012/11

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

Abstract

ASJC Scopus subject areas

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