JBrowse Desktop

This page provides a reference guide for "Desktop JBrowse" or "JBrowse Desktop", which is a electron application that was unveiled for the release of JBrowse 1.12.0.

The operation of JBrowse Desktop is comparable to other desktop genome browsers like IGV or IGB, and it can be run without setting up a webserver (most of the time normal jbrowse runs on apache and is viewed in a web browser). In contrast, JBrowse Desktop is a simple exe file that can easily be run locally on Windows or Mac.

Installation

At the most basic level, setting up JBrowse Desktop consists of:

• Downloading a zip file script from jbrowse.org e.g. from http://jbrowse.org/jbrowse-1-12-1/ and OSX and a Windows version exsits JBrowse-1.12.1-desktop-osx.zip and JBrowse-1.12.1-desktop-win.zip
• After downloading unzip the file to somewhere. There is no official uninstaller but you can move it to the Program files or Applications directory as needed.

Note: on Mac, you can alternatively use Homebrew and run `brew cask install jbrowse` which will download and place jbrowse in your Application directory

Overview of JBrowse Desktop

When you run JBrowse Desktop you will see a sort of "welcome screen" that gives you several options

• View Volvox sample data
• Open sequence file, this allows you to open FASTA, Indexed FASTA, or .2bit
• Open data directory, this allows you to open a data directory that has been prepared with normal jbrowse tools

Note: it is highly recommended to use Indexed FASTA (selecting both a fasta and a fai file generated by `samtools faidx file.fasta`) or 2bit. Even small genomes with normal FASTA will be much slower!

Limitations

• The "Save session" function will not save some configuration customizations, so if you have advanced customizations it would be recommended to make a data directory by hand the trackList.json and tracks.conf format files
• If you open a data directory on the web, then "Save session" won't work

Features

• Can open files from shared network folders and external hard drives on both windows and mac
• Can open files from remote URLs
• Can open data directories from remote URL
• Saves "sessions" to the OS "application data" folders
• Has a "home screen" that lists previous sessions

Technical details

The folder where sessions are saved is generally

• OSX - "~/Library/Application Support/jbrowse"
• Windows - "C:\Users\username\AppData\Roaming\jbrowse"

Tested platforms

• OSX Mavericks
• macOS sierra
• Windows 7
• Windows 10

Note: JBrowse Desktop doesn't work on windows XP and Vista (all electron apps are limited to Windows 7+)

External Links

• JBrowse: a dynamic web platform for genome visualization and analysis paper