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PMID: 23376193 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Using GBrowse 2.0 to visualize and share next-generation sequence data.

Briefings in bioinformatics ·Vol. 14 ·No. 2 ·2013-03-00 ·Pages 162-71

Stein LD

Abstract

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data.

MeSH Terms
Animals Computational Biology Computer Graphics Computer Storage Devices Data Display Databases, Genetic/statistics & numerical data High-Throughput Nucleotide Sequencing/statistics & numerical data Humans Information Storage and Retrieval Internet Sequence Alignment/statistics & numerical data Software
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Stein Lincoln D
Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada. lincoln.stein@gmail.com
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11 references, click to expand
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Article Info
Journal
Briefings in bioinformatics
Abbr.
Brief Bioinform
ISSN
1477-4054
DOI
10.1093/bib/bbt001
Email
lincoln.stein@gmail.com
Published
2013-03-00
Epub
2013-00-01
Pages
162-71
Language
English
Region
England
NLM ID
100912837
PMCID
PMC3603216
Subset
IM
Grants
PHS HHS · P41 G02223 · United States
External Links
PubMed source DOI: 10.1093/bib/bbt001 PMC Full Text View journal details
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