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/debateResearchpeer-review

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

Fingerprint

Antimalarials
Browsing
Nucleotides
Polymorphism
Sequencing
Genes
Drug Resistance
Single nucleotide Polymorphism
Plasmodium falciparum
Differentiate
Pharmaceutical Preparations
Balancing
Deletion
Insertion
Single Nucleotide Polymorphism
Genomics
Software
Gene
Real-time
Demonstrate

Cite this

Preston, Mark D. ; Manske, Magnus ; Horner, Neil ; Assefa, Samuel ; Campino, Susana ; Auburn, Sarah ; Zongo, Issaka ; Ouedraogo, Jean Bosco ; Nosten, Francois ; Anderson, Tim ; Clark, Taane G. / VarB : A variation browsing and analysis tool for variants derived from next-generation sequencing data. In: Bioinformatics. 2012 ; Vol. 28, No. 22. pp. 2983-2985.
@article{8b92c4c43a0b448f93c04b93b4ee149d,
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.}",
year = "2012",
month = "11",
doi = "10.1093/bioinformatics/bts557",
language = "English",
volume = "28",
pages = "2983--2985",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "22",

}

Preston, MD, Manske, M, Horner, N, Assefa, S, Campino, S, Auburn, S, Zongo, I, Ouedraogo, JB, Nosten, F, Anderson, T & Clark, TG 2012, 'VarB: A variation browsing and analysis tool for variants derived from next-generation sequencing data', Bioinformatics, vol. 28, no. 22, pp. 2983-2985. https://doi.org/10.1093/bioinformatics/bts557

VarB : A variation browsing and analysis tool for variants derived from next-generation sequencing data. / Preston, Mark D.; Manske, Magnus; Horner, Neil; Assefa, Samuel; Campino, Susana; Auburn, Sarah; Zongo, Issaka; Ouedraogo, Jean Bosco; Nosten, Francois; Anderson, Tim; Clark, Taane G.

In: Bioinformatics, Vol. 28, No. 22, 11.2012, p. 2983-2985.

Research output: Contribution to journalComment/debateResearchpeer-review

TY - JOUR

T1 - VarB

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.

UR - http://www.scopus.com/inward/record.url?scp=84869460203&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bts557

DO - 10.1093/bioinformatics/bts557

M3 - Comment/debate

VL - 28

SP - 2983

EP - 2985

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 22

ER -