Edit Tool data: JBrowse

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The Basics[edit]

Name:
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Status:
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Tool classification or features:	Genome visualization
Platform:	If the tool linux unix os x windows web vm cloud
Brief description:	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.
Open source:
Software licence:
Type of input data	e.g. genomic sequence; taxonomic group; protein identifier; anatomy ontology, etc.
Input formats:	[[GFF3]], BED, FASTA, WIG, BedGraph, Bio::DB::*, UCSC, Wiggle, BigWig, BAM
Output formats:
Programming language(s)
Intended usage
First public release
Use standard tool display template?	yes

Files[edit]

Logo (file name)	enter the name of the file on the GMOD wiki, e.g. CoolAppLogo.png JBrowseLogo.png
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Contact details[edit]

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Links[edit]

The majority of links related to the tool should be added using the interface at the bottom of the page.

Download text	If there is not a simple download URL for downloading the tool, please enter download instructions here. Download URLs can be entered in the 'Links' section below.
Download source code text	If there is not a simple download URL for downloading the source code for the tool, please enter download instructions here. URLs can be entered in the 'Links' section below.

Materials[edit]

Publications	* JBrowse: a next-generation genome browser (2009)<ref name="PMID:19570905">JBrowse: a next-generation genome browser </ref> Setting up the JBrowse genome browser (2010)<ref name="PMID:21154710">Setting up the JBrowse genome browser </ref> Visualizing next-generation sequencing data with JBrowse (2013)<ref name="PMID:22411711">* Visualizing next-generation sequencing data with JBrowse</ref> * JBrowse: a dynamic web platform for genome visualization and analysis (2016)<ref name="PMID: 27072794">* JBrowse: a dynamic web platform for genome visualization and analysis</ref>
Presentations	* April 2013 - Bio-IT World, Robert Buels: [[Media:JBrowse_bioit_world_apr2013.pdf\|PDF]] * August 2012 - presentation given as part of the [[2012 GMOD Summer School]]: [[Media:JBrowse_gmod_aug2012.pdf\|PDF]] * April 2012 - GMOD 2012 Community Meeting, Robert Buels: [[Media:RBuels_JBrowse_apr2012.pdf\|PDF]] * January 2012 - Plant and Animal Genome (PAG) XX: [[Media:Rbuels_jbrowse_pag2012.pdf\|PDF]] * April 2010 - UCSC genome browser group ("genecats") meeting: [[Media:JBrowse-UCSC-4-21-10.pdf\|PDF]] * August 2009 - [[August 2009 GMOD Meeting\|GMOD Community Meeting]]: [[ August 2009 GMOD Meeting#JBrowse \| Talk summary ]]
Tutorials	;[[JBrowse Tutorial]] covering installation and configuration :part of the [[2013 GMOD Summer School]] ;[http://jbrowse.org/code/latest-release/docs/tutorial/ Getting Started with JBrowse Tutorial] :part of the JBrowse documentation ;[[Media:Exploring_structural_variation_in_the_tomato_clade_using_JBrowse.pdf \| Exploration of structural variation in the tomato clade using JBrowse]] :Tutorial explaining how to browse structural variants from the [http://www.tomatogenome.net 150+ tomato genome resequencing project] using JBrowse

Extra Textual Goodies[edit]

Any introductory text for users	The [http://jbrowse.org/code/latest-release/docs/tutorial/ JBrowse Quick-Start Tutorial] provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
Software prerequisites	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 [http://jbrowse.org/code/latest-release/docs/tutorial/ JBrowse Quick-Start Tutorial] provides a basic step-by-step recipe for quickly getting up and running with JBrowse. 1. [http://jbrowse.org/install/ 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 <code>/var/www</code>. cd /var/www unzip JBrowse-*.zip '''Make sure you have permissions to write to the contents of the <code>jbrowse/</code> directory you have just created.''' 3. Run the automated-setup script, <code>./setup.sh</code>, which will attempt to install all of JBrowse's (modest) prerequisites for you in the <code>jbrowse/</code> directory itself. Note that <code>setup.sh</code> does not need to be run as root or with <code>sudo</code>. For help troubleshooting failures of setup.sh, see [[JBrowse Troubleshooting]]. 4. Visit JBrowse on your machine, substituting the <nowiki>http://(your_machine/path_to_jbrowse)/index.html?data=sample_data/json/volvox</nowiki>. 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: * [[JBrowse Configuration Guide#Reference Sequences\|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database) * [[JBrowse Configuration Guide#Feature Tracks\|Feature Tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser) * [[JBrowse Configuration Guide#Image Tracks\|Image Tracks]] (e.g. from WIG files) * [[JBrowse Configuration Guide#Wiggle_Tracks\|Wiggle/BigWig Tracks]] * [[JBrowse Configuration Guide#Name_Searching_and_Autocompletion \| Name Search and Autocompletion]] * [[JBrowse Configuration Guide#Removing Tracks\|Removing tracks]] * [[JBrowse Configuration Guide#Compressing data on the server\|Compressing data stored on the server]] * [[JBrowse Configuration Guide#URL Control \| URL control ]] * [[JBrowse Configuration Guide#Faceted Track Selection \| Faceted track selection ]] * [[JBrowse Configuration Guide#Anonymous Usage Statistics \| Anonymous usage statistics ]] Additional topics: * [[JBrowseDev/Using a Database With JBrowse\|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 <code>jbrowse_conf.json</code> 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	[http://gmod.org/wiki/JBrowse_Configuration_Guide JBrowse configuration reference] [http://jbrowse.org/code/latest-release/docs/tutorial JBrowse quick start] *[http://gmod.org/wiki/JBrowse_FAQ JBrowse setup FAQ]
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See also	Any extra information, links, etc.
Extra items for component box	{{GitcComponent}}

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[[Category:GMOD Components]] [[Category:AJAX]] [[Category:JBrowse]]

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