In order to display your data, JBrowse 2 needs to know about the reference genome for your organism of interest and needs to have tracks created that reference your data sources. This guide will show you how to set those up using the JBrowse 2's graphical configuration editing.
You can also do this configuration with JBrowse CLI. See that guide here.
This tutorial requires having the following software installed
Starting JBrowse 2 admin server
The JBrowse CLI contains a tool called
admin-server. This will act as a web
server for JBrowse 2 and will write any changes made in JBrowse 2 to a config
admin-server is meant to be run only temporarily to help you set up
your config, it is not used for serving your jbrowse instance in production.
admin-server launches an instance of JBrowse 2 in "admin mode", which then
- Add and edit assemblies with the "Assembly manager"
- Add tracks and edit tracks
- Add and edit connections
All of these changes will be written by the server to the JBrowse config file
config.json) located in the JBrowse instance. This is something that
can only be done while the
admin-server is running, which again, is only meant
to be temporary!
To start the
admin-server, navigate into your JBrowse 2 directory and run
This will then generate a link that you can visit in your web browser
Note: the admin-server is meant to be used temporarily for configuration, not in production
Adding a genome assembly
A key first step in configuring a genome browser is adding an assembly to view.
In order to do this, use the navigation bar to open up the Assembly Manager
Admin > Open Assembly Manager).
This opens up a table which can be used to create, edit, and delete assemblies in your application
Let's add the hg38 human reference genome to our JBrowse 2 application.
Press the "Add New Assembly" button, and enter
hg38 as the assembly name in
the text field
Click on "Create New Assembly". Great, we've added an assembly! Now, in the configuration editor, add an alias, and configure the adapter to point the hg38 genome hosted by JBrowse:
- fasta index:
Figure showing the settings
After clicking the back arrow to return to the table of assemblies, we see that we have successfully added the hg38 assembly.
Figure showing the assembly manager
The assembly can be edited or deleted, but for now we will return to the application.
Editing a genome assembly
After you've added a genome assembly, you can use the pencil icon button in the Assembly manager to edit that assembly. You can also delete assemblies from the assembly manager.
Adding a track
To add a new track or connection, you can use the menu bar in the app to open
the form for adding a track
File > Open Track:
Alternatively, you can use the action button (circular "+") inside the track selector to access the "Add track" form.
In the "Add track" form, you can provide a URL to a file to load. Opening files from your local machine is not supported currently in the JBrowse 2 web app (JBrowse desktop does allow this, though, and this functionality may be added in some form in the future)
Paste a URL to a file and optionally provide an index file URL too. The following file formats are supported
- indexed BAM
- indexed CRAM
- Hi-C (Juicebox)
For tabix files, TBI or CSI indexes are allowed. CSI or BAI is allowed for BAM. Only CRAI is allowed for CRAM. The index will be inferred for BAI or TBI files as e.g. filename+'.bai'. If it is different from this, make sure to specify the index file explicitly.
Editing a track
First we will open a Linear Genome View using the navigation bar
File > Add > Linear Genome View), and click on the "Select Tracks" button.
The configuration settings are accessible by clicking on the ellipses by each track.
Figure showing the configuration editor
Open the configuration editor for the track by clicking on the "Settings" button shown above. You can use the configuration editor to live-edit any configurable value for a given track.
This quickstart showed how to launch the
admin-server in the JBrowse CLI to
perform graphical configuration of your application. Specifically, we looked at
how to access and use the assembly manager, as well as how to access the
configuration editor for tracks. Importantly, all tracks have different
configuration options available in the configuration editor.
Make sure to take a look at any tracks you add to JBrowse 2 that you might want to further configure!