GMOD
JBrowse
Status
- Mature release
- Development: active
- Support: active
Licence
Resources
Contents
- 1 About JBrowse
- 2 Downloads
- 3 Using JBrowse
- 4 Upgrading JBrowse
- 5 Documentation
- 6 Publications, Tutorials, and Presentations
- 7 Contacts and Mailing Lists
- 8 JBrowse in the wild
- 9 JBrowse Development
- 10 More on JBrowse
About JBrowse
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.
Features
- 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 JBrowse website.
Screenshots
Downloads
Using JBrowse
The JBrowse Quick-Start Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
System Requirements
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 JBrowse Troubleshooting.
Installation
The JBrowse Quick-Start Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
- Download 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 JBrowse
Troubleshooting.
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!
Configuration
See the JBrowse Configuration Guide for information on:
- Formatting reference sequences (e.g. from FASTA files, or a Chado database)
- Feature Tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
- Image Tracks (e.g. from WIG files)
- Wiggle/BigWig Tracks
- Name Search and Autocompletion
- Removing tracks
- Compressing data stored on the server
- URL control
- Faceted track selection
- Anonymous usage statistics
Additional topics:
Upgrading JBrowse
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.
Documentation
Publications, Tutorials, and Presentations
Publications on or mentioning JBrowse
- JBrowse: a next-generation genome browser (2009)[1]
- Setting up the JBrowse genome browser (2010)[2]
- Visualizing next-generation sequencing data with JBrowse (2013)[3]
- JBrowse: a dynamic web platform for genome visualization and analysis (2016)[4]
Tutorials
JBrowse Tutorial covering installation and configuration
part of the 2013 GMOD Summer
School
Getting Started with JBrowse
Tutorial
part of the JBrowse documentation
Exploration
of structural variation in the tomato clade using JBrowse
Tutorial explaining how to browse structural variants from the
150+ tomato genome resequencing project using JBrowse
Presentations
- April 2013 - Bio-IT World, Robert Buels: PDF
- August 2012 - presentation given as part of the 2012 GMOD Summer School: PDF
- April 2012 - GMOD 2012 Community Meeting, Robert Buels: PDF
- January 2012 - Plant and Animal Genome (PAG) XX: PDF
- April 2010 - UCSC genome browser group (“genecats”) meeting: PDF
- August 2009 - GMOD Community Meeting: Talk summary
Contacts and Mailing Lists
Please direct questions and inquiries regarding JBrowse to the mailing lists below.Requests for help should be directed to gmod-ajax@lists.sourceforge.net.
| Mailing List Link | Description | Archive(s) | |
| JBrowse | <a href=”https://lists.sourceforge.net/lists/listinfo/gmod-ajax” | ||
| class=”external text” rel=”nofollow”>gmod-ajax</a> | JBrowse help and general questions. | <a href=”http://gmod.827538.n3.nabble.com/JBrowse-Support-f815920.html” |
class=”external text” rel=”nofollow”>Nabble</a> (2010/05+), Sourceforge | | | jbrowse-dev | JBrowse development discussions. | Nabble (2011/08+) |
gmod-ajax@lists.sourceforge.net
JBrowse in the wild
Public installations of JBrowse:
- Genomes Unzipped: Public Personal Genomics
- BeetleBase
- The Jane-Ome, medicinal marijuana project
- Ice Man Genome Browse the genome of Ötzi the ice man
JBrowse Development
Current status
The JBrowse source code repository 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 tutorial on how to get started with this style of development.
More on JBrowse
- ↑ *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
</span>
web +
http://jbrowse.org/install/ +, http://jbrowse.org +, http://twitter.com/usejbrowse +, http://github.com/GMOD/jbrowse +, http://jbrowse.org/demos +, http://icemangenome.net/%E2%80%8E +, http://genomesunzipped.org/jbrowse +, http://beetlebase.org + and http://www.medicinalgenomics.com/the-jane-ome/ +
JBrowse is a genome browser with a fully d … 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.
Features
- 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 Ötzi the ice man +