Connections

A connection is a reusable pointer to an external track hub or data directory. Once opened, JBrowse fetches the hub's track list automatically and adds those tracks to the track selector — no manual configuration of each track is needed. Closing a connection removes all of its tracks.

JBrowse supports two built-in connection types:

  • UCSC Track Hub — any UCSC Genome Browser track hub reachable over the network
  • JBrowse 1 data directory — a legacy JBrowse 1 data directory with a trackList.json

Opening a connection via the UI

Use the menu bar: File → Open connection...

A form will appear asking for the connection URL and type. Paste the hub URL (see below for the format), choose the connection type, and click Submit.

Tracks from the connection will appear in the track selector under a category named after the connection.

UCSC track hub URL format

The URL must point directly to the hub.txt file of the hub, for example:

https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt

Public hubs are listed in the UCSC Public Hub directory. Each hub listed there has a "URL" column — paste that URL into the connection form.

Assembly names

JBrowse matches hub tracks to assemblies by genome ID. If the hub targets an assembly not already configured in your JBrowse instance, those tracks will not appear. You can filter by assembly name in the connection form.

JBrowse 1 connection URL format

The URL must point to the JBrowse 1 data directory containing trackList.json, for example:

https://myhost/jbrowse1/data/

You also need to supply the assembly name that this data directory corresponds to.

Adding a connection via the CLI

# UCSC track hub
jbrowse add-connection https://example.com/hub.txt \
  --type UCSCTrackHubConnection \
  --name "My Hub"

# JBrowse 1 data directory
jbrowse add-connection https://myhost/jbrowse1/data/ \
  --type JBrowse1Connection \
  --assemblyNames hg19 \
  --name "JBrowse 1 data"

See jbrowse add-connection --help or the CLI reference for all options.