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Connections

TL;DR: A connection is a reusable pointer to an external track hub or data directory. Point JBrowse at a hub once and its tracks become available in the track selector.

JBrowse supports three built-in connection types:

Connections in the track selector

Every connection appears as its own category in the track selector, listed below your regular tracks and named after the connection.

A connection is loaded lazily: expanding its category fetches the hub's track list. This keeps large hubs (which can contain thousands of tracks) out of the way until you want them. Once expanded, its tracks appear underneath and you open them with their checkboxes like any other track.

Because loading only happens on expand, adding several connections is cheap. Expand the one you want; leave the rest collapsed.

Opening a connection

Open the form from either route:

  • Menu bar: File → Open connection...
  • Track selector's hamburger menu → Connections... → Add connection...

Paste the hub URL (see below for the format), choose the connection type, and submit. A newly added connection loads right away, so its tracks appear immediately.

Connections and saved sessions

Opening a track from a connection remembers it in your session, so after a page reload it reopens immediately without re-fetching the whole hub. The connection's category shows collapsed; expand it again to browse the rest.

Only the tracks you opened are stored, so sharing or saving a session that uses a connection stays lightweight even when the underlying hub is huge.

Removing a connection

Open the track selector's hamburger menu → Connections... → Delete connections... and choose the connection to remove.

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; paste the URL from its "URL" column into the connection form.

JBrowse matches hub tracks to assemblies by genome ID. Tracks targeting an assembly not configured in your JBrowse instance will not appear. You can filter by assembly name in the connection form.

JBrowse 1 connection URL format

For the legacy JBrowse 1 connection type, point the URL at the JBrowse 1 data directory containing trackList.json (e.g. https://myhost/jbrowse1/data/) and supply the assembly name it corresponds to. See the JBrowse1Connection config docs for details.

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.

See also