JBrowse2

This page is under active development

Status

• Mature release
• Development: active
• Support: active

Licence

Apache 2

Resources

• Home page

• Download

• Source code

• Demo server

About JBrowse 2

JBrowse is a genome browser with a fully dynamic AJAX interface, continuing development as the successor to GBrowse and JBrowse. 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 JBrowse2 website.

Downloads

• Download JBrowse2.

• Download the source code for JBrowse2.

Using JBrowse 2

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.

1. 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:

• Using an Existing Database with JBrowse

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

• JBrowse configuration reference
• JBrowse quick start
• JBrowse setup FAQ

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	gmod-ajax	JBrowse help and general questions.	Nabble (2010/05+), Sourceforge
	jbrowse-dev	JBrowse development discussions.	Nabble (2011/08+)

gmod-ajax@lists.sourceforge.net

JBrowse 2 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 2

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• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

• "embedded" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
• "desktop" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.