Config editing quick start — graphical interface

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.

note

You can also do this configuration with JBrowse CLI. See that guide here.

Pre-requisites

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 file. The 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.

The admin-server launches an instance of JBrowse 2 in "admin mode", which then lets you

  • 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 (usually 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

## Start the admin-server
jbrowse admin-server

This will then generate a link that you can visit in your web browser

JBrowse CLI admin-server output

warning

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

Assembly manger

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

Assembly manager page for adding an assembly

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: https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz
  • fasta index: https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai
  • gzi: https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi

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:

JBrowse 2 file menu with  menu item

Alternatively, you can use the action button (circular "+") inside the track selector to access the "Add track" form.

JBrowse 2 action button

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

  • tabix-indexed VCF
  • tabix-indexed BED
  • tabix-indexed GFF
  • indexed BAM
  • indexed CRAM
  • BigWig
  • BigBed
  • 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.

Additional resources

There are a number of additional features for configuring JBrowse 2. Make sure to refer to the config guide for topics such as adding tracks or adding an assembly with the CLI

Conclusion

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!