Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Apr 12:17:66.
doi: 10.1186/s13059-016-0924-1.

JBrowse: a dynamic web platform for genome visualization and analysis

Robert Buels  1 , Eric Yao  1 , Colin M Diesh  2 , Richard D Hayes  3   4 , Monica Munoz-Torres  3 , Gregg Helt  3   5 , David M Goodstein  3   4 , Christine G Elsik  2 , Suzanna E Lewis  3 , Lincoln Stein  6   7 , Ian H Holmes  8   9
Affiliations

JBrowse: a dynamic web platform for genome visualization and analysis

Robert Buels et al. Genome Biol. .

Abstract

Background: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.

Results: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication.

Conclusions: JBrowse is a mature web application suitable for genome visualization and analysis.

Keywords: Bioinformatics; Browser; Genome.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
JBrowse screenshot showing (for Volvox test dataset) the hierarchical track selector (left-hand pane) and (from top to bottom in the right-hand pane) menu bar, location bar, navigation bar, CanvasFeatures track (with NeatCanvasFeatures plugin), HTMLFeatures track (mRNAs; with NeatHTMLFeatures plugin), Reference Sequence track, Wiggle/XYPlot track, and Wiggle/Density track
Fig. 2
Fig. 2
JBrowse screenshot captured with PhantomJS and showing (for Volvox test dataset) the hierarchical track selector (left-hand pane) and (from top to bottom in the right-hand pane) Reference Sequence track, SNPCoverage track, Alignments2 track, and HTMLVariants tracks (with NeatHTMLFeatures plugin)
Fig. 3
Fig. 3
JBrowse screenshot showing large track-set faceted track selector from modENCODE test dataset
Fig. 4
Fig. 4
JBrowse “combination track” workflow. Combination tracks are created via the Track menu (a), presenting an empty track as a drop target (b). Tracks can then be dragged onto the combination track (c). The second and subsequent tracks bring up a combination dialog (d), with options for set union, intersection, and difference. The results of the set operation are shown in the combination track (e)
See this image and copyright information in PMC

References

    1. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. 2009;19:1630–8. doi: 10.1101/gr.094607.109. - DOI - PMC - PubMed
    1. Skinner ME, Holmes IH. Setting up the JBrowse genome browser. Curr Protoc Bioinformatics. 2010;Chapter 9:Unit 9.13. - PMC - PubMed
    1. Westesson O, Skinner M, Holmes I. Visualizing next-generation sequencing data with JBrowse. Brief Bioinform. 2013;14:172–7. doi: 10.1093/bib/bbr078. - DOI - PMC - PubMed
    1. Down TA, Piipari M, Hubbard TJP. Dalliance: interactive genome viewing on the web. Bioinformatics. 2011;27:889–90. doi: 10.1093/bioinformatics/btr020. - DOI - PMC - PubMed
    1. Hammerbacher lab, Pileup.js. https://github.com/hammerlab/pileup.js. Accessed 28 Mar 2016.

Publication types