Genome Assembly Support

In order to correctly categorise TrackHubs into the Track Hub Registry it is essential to tag hubs against the right assembly version during the submission process. The Track Hub Registry attempts to normalise any given assembly name into a suitable Genome Collection Accession (GCA) during submission e.g. the UCSC assembly name hg19 is automatically converted into GCA_000001405.1. All hubs registered with the Track Hub Registry should have a GCA available in the Genome Assembly Database to map to and is a current requirement of submitting to the registry. All modern assemblies should conform to this requirement.

The Track Hub Registry promotes interoperability of hubs in all major genome browsers. As such we recommend you use the UCSC assembly name where available.

Mapping Track Hub Assembly Names

When a Genome is Available in the UCSC Genome Browser

If your genome is in UCSC you should use the UCSC accession in your genomes.txt file as shown below:

genome hg19
trackDb hg19/trackDb.txt

The Track Hub Registry will normalise this into a suitable GCA accession. For genomes with multiple patch releases i.e. GRCh37/hg19, GRCh38/hg38 and GRCm38/mm10 we normalise to the original GCA used for that assembly version.

When a Genome is not Available in the UCSC Genome Browser

If you genome is not in UCSC we recommend you use the assembly name as present in the GCA record. You can find this either by querying the NCBI Genome list for your species of interest and clicking on the Organism/Name or Assemblies links.

For example Arabidopsis thaliana is a genome not available in UCSC. Searching at NCBI will lead you to the active assembly name TAIR10 and the accession GCA_000001735.1. Your genomes.txt file should be structured as shown below:

genome TAIR10
trackDb TAIR10/trackDb.txt

When submitting the hub to the Track Hub Registry you must tell the registry the mapping between TAIR10 and GCA_000001735.1 like so:

{ 
  "url" : "http://www.domain.com/test/hub.txt", 
  "assemblies": {
    "TAIR10": "GCA_000001735.1"
  }
}

More details are available from the submissions API reference.