Contributing Tracks to the UCSC Genome Browser

Contributed tracks are annotations produced by research groups and integrated into the default Genome Browser view on GenArk assemblies. This page describes how to prepare and submit them.

Submission workflow

1. Develop and test your annotations as a track hub hosted on a web server you control.
2. Organize the hub following the directory structure below.
3. Send the URL of your hub.txt file to the Genome Browser team for review and inclusion.

Directory structure

Each assembly gets its own subdirectory named by its NCBI accession identifier (GCA_ or GCF_). Data files and the trackDb.txt must use the same file names in every assembly directory. This allows a single trackDb.txt to work across all assemblies.

+-- hub.txt
+-- genomes.txt
+-- documentation.html
+-- GCA_000260495.2/
|   +-- trackDb.txt
|   +-- myTrack.bb
|   +-- myTrackDocs.html
+-- GCF_014441545.1/
|   +-- trackDb.txt
|   +-- myTrack.bb
|   +-- myTrackDocs.html
+-- GCF_014108235.1/
|   +-- trackDb.txt
|   +-- myTrack.bb
|   +-- myTrackDocs.html

Requirements

• Assembly naming: Directory names and assembly identifiers in genomes.txt must be NCBI GenBank or RefSeq accession identifiers (e.g., GCA_000260495.2 or GCF_014441545.1). A full list of GenArk assemblies is available at the assembly hub list.
• Data formats: Annotation data must be in bigBed, bigWig, or another supported track type.
• Uniform file names: Use the same file names for data files and trackDb.txt across all assembly directories (e.g., myTrack.bb everywhere, not myTrack.GCA_000260495.2.bb).
• Documentation: Every track must include an HTML documentation page (see Track documentation below).

Example hub.txt

hub myProjectHub
shortLabel My Contributed Tracks
longLabel Contributed annotation tracks for GenArk assemblies
email user@example.edu
genomesFile genomes.txt
descriptionUrl documentation.html

The descriptionUrl page provides an overall description of the hub or research project. For details on hub.txt settings, see the Track Hub User Guide.

Example genomes.txt

genome GCA_000260495.2
trackDb GCA_000260495.2/trackDb.txt

genome GCF_014441545.1
trackDb GCF_014441545.1/trackDb.txt

genome GCF_014108235.1
trackDb GCF_014108235.1/trackDb.txt

One block per assembly, separated by a blank line. The genome value is the NCBI accession identifier, and trackDb points to the trackDb.txt file in that assembly's subdirectory.

Example trackDb.txt

track myTrack
shortLabel My Track
longLabel My contributed annotation track for GenArk assemblies
type bigBed 9 +
visibility dense
bigDataUrl myTrack.bb
searchIndex name
html myTrackDocs

Because data files have the same name in every assembly directory, this identical trackDb.txt works for all assemblies. The bigDataUrl is a relative path to the data file in the same directory. The html setting points to the track documentation page (without the .html extension). For the full list of trackDb settings, see the trackDb documentation.

Track documentation

Every track must have an HTML documentation page. Place it in each assembly directory with the filename referenced by the html setting in trackDb.txt (e.g., myTrackDocs.html). If you omit the html setting, the browser looks for [trackName].html in the same directory as the trackDb.txt file.

Structure your documentation page with these sections:

• Description — What the annotation represents.
• Methods — How the annotation was generated.
• Credits — Who produced the data.
• References — Relevant publications or resources.

A template documentation page is available as a starting point. For an example of a completed track description, see the recombination rate track page.

Live example

An example contributed track hub with EVA SNP Release 8 data on five GenArk assemblies is available for reference:

• Hub URL: hub.txt
• View in browser: GCF_000971095.1 (swan goose) with EVA SNP track

Next steps

Once your hub is ready, contact the UCSC Genome Browser team with your hub.txt URL. You can test it first by loading it via My Data > Track Hubs in the browser. The team will review your submission and work with you to integrate the tracks.

For general information about track hubs, see the Track Hub User Guide. For best practices, see the Public Hub Guidelines.