Using the genome browser

Screenshot 1: The genome browser for GCA_911387925.2

G-nom integrates a fully featured genome browser powered by JBrowse2. G-nom automatically generates track configs for all genomic annotations and mappings uploaded for a given assembly. Some analyses are parsed to create custom tracks with uniform color schemes across all assemblies (i.e. LTR/Copia elements identified by RepeatMasker will always be colored blue). Tracks use the names provided on import. G-nom also generates tabix indices automatically, enabling full-text search of annotation and mapping feature i.e. by their feature IDs.

You can find the browser under the URL /browser or by following the link in the navbar. Upon loading the page, you will be prompted to select one of the assemblies stored in G-nom. Once you click "Launch Browser", you will be re-directed to a page with a pre-populated JBrowse genome browser. Alternatively, the assembly page provides a button in the "Genome Browser" section to jump to pre-populated JBrowse genome browser for the assembly instantly.

For further usage instruction, please refer to the Jbrowse2 Documentation.

Data access

Genome Browser tracks inherit the access policy enforced by their associated assembly. G-nom will throw a 403 Error when users try to access data they are not permitted to read.

Session persistence

JBrowse allows you to store and load sessions in .json files, requiring you to download / upload them from your device.

G-nom currently does not store sessions server-side. This is subject to change in a future update.