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Mature release
Development: active
Support: active
JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse is javascript-based and does almost all of its work directly in the user's web browser, with minimal requirements for the server.
Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed.
Scales easily to multi-gigabase genomes and deep-coverage sequencing.
Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, and more.
BAM, BigWig, and VCF data are displayed directly from the compressed binary file with no conversion needed.
Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.
Visit the .
provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
JBrowse requires libpng, Zlib, and GD development libraries, plus make and a C compiler.
On Ubuntu, you can install these prerequisites using the command:
sudo apt-get install libpng-dev libgd2-noxpm-dev build-essential
For tips on installing these baseline libraries, see .
provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
onto your web server.
2. Unpack JBrowse into a directory that is served by your web browser.
On many systems, this defaults to /var/www.
cd /var/www
unzip JBrowse-*.zip
Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.
3. Run the automated-setup script, ./setup.sh, which will attempt to install all of JBrowse's (modest) prerequisites for you in the jbrowse/ directory itself.
Note that setup.sh does not need to be run as root or with sudo.
For help troubleshooting failures of setup.sh, see .
4. Visit JBrowse on your machine, substituting the http://(your_machine/path_to_jbrowse)/index.html?data=sample_data/json/volvox.
If you can see the included Volvox example data, you are ready to configure JBrowse to show your own data!
for information on:
(e.g. from FASTA files, or a Chado database)
(e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
(e.g. from WIG files)
Additional topics:
To upgrade an existing JBrowse (1.3.0 or later) to the latest version, simply move its data directory (and jbrowse_conf.json if you are using it) into the directory of a newer JBrowse, and the new JBrowse will display that data.
To upgrade a 1.2.x JBrowse, copy its data directory into the new JBrowse directory, and point your browser at compat_121.html in the new JBrowse directory, instead of index.html.
If you are upgrading from a version of JBrowse older than 1.2.0, a fresh installation is required.
JBrowse: a next-generation genome browser (2009)
Setting up the JBrowse genome browser (2010)
Visualizing next-generation sequencing data with JBrowse (2013)
JBrowse: a dynamic web platform for genome visualization and analysis (2016)
covering installation and configuration
part of the
part of the JBrowse documentation
Tutorial explaining how to browse structural variants from the
using JBrowse
April 2013 - Bio-IT World, Robert Buels:
August 2012 - presentation given as part of the :
April 2012 - GMOD 2012 Community Meeting, Robert Buels:
January 2012 -
Plant and Animal Genome (PAG) XX:
April 2010 - UCSC genome browser group ("genecats") meeting:
August 2009 - :
Please direct questions and inquiries regarding JBrowse to the mailing lists below.Requests for help should be directed to .
Mailing List Link
Description
Archive(s)
JBrowse help and general questions.
(2010/05+),
JBrowse development discussions.
(2011/08+)
gmod-ajax@lists.sourceforge.net
Public installations of JBrowse:
Browse the genome of ?tzi the ice man
is kept on GitHub.
Please feel very free to fork the code on GitHub and make modifications and improvements, submitting pull requests.
GitHub has a very nice
on how to get started with this style of development.
*JBrowse: a next-generation genome browser
*Setting up the JBrowse genome browser
* Visualizing next-generation sequencing data with JBrowse
* JBrowse: a dynamic web platform for genome visualization and analysis
JBrowse is a genome browser with a fully dJBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse is javascript-based and does almost all of its work directly in the user's web browser, with minimal requirements for the server.
Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed.
Scales easily to multi-gigabase genomes and deep-coverage sequencing.
Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, and more.
BAM, BigWig, and VCF data are displayed directly from the compressed binary file with no conversion needed.
Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.ets from a single low-cost cloud instance.
and Browse the genome of ?tzi the ice man
, BedGraph
, Bio::DB::*
JBrowseLogo.png
JBrowse demos
, Ice Man Genome
, Genomes Unzipped: Public Personal Genomics
, BeetleBase
and The Jane-Ome, medicinal marijuana project
, social media
, source code
, demo server
and wild URL
Genome visualization
Javascript
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