Genome Reference Consortium

The goal of the Genome Reference Consortium (GRC) is to ensure that the human, mouse and zebrafish reference assemblies are biologically relevant by closing gaps, fixing errors and representing complex variation.

The GRC is a collaboration between the The Wellcome Trust Sanger Institute (WTSI), theThe Genome Institute at Washington University ( TGI), the European Bioinformatics Institute (EBI) and the The National Center for Biotechnology Information (NCBI). The NCBI hosts the GRC home pages. News about the GRC activities can be found in our blog. If you want to keep up with major and minor assembly releases and other events, subcribe to our announcement list.

Upcoming assembly releases and remapping

The new human genome assembly update, GRCh38.p2, is now publicly available.More information can be found in our blog.A new zebrafish assembly, GRCz10, has now been released. This new assembly release will benefit from hundreds of gap closures, adjustment of clone overlaps and new clones being added. On top of this, clones and clone contigs are being re-ordered and reoriented according to data from optical mapping and additional SATmap markers. You can read more about this here.

When the GRC produces a new major assembly release, this alters the chromosome coordinates. Although we strongly recommend to map all features de novo, it is possible to convert the chromosome coordinates of annotation based on an older release into the coordinates for the equivalent sequence in a new release using the NCBI's Remap tool. The sequence alignments between major releases that underlie the Remap tool are available from the GRC website; for instance, alignments between the mouse MGSCv37 and GRCm38 assemblies are available via the GRC mouse page following the ftp link.

View GRC annotation in genome browsers via the GRC track hub

The GRC are providing their curation for reference genomes via a weekly updated track hub, which will allow you to view the data in a range of genome browsers, including Ensembl and UCSC. The hub is located at http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt.The provision of DAS sources for the same purpose is discontinued.

The GRC generates a range of annotation on the reference genomes it curates. This annotation describes assembly and quality issues with these genomes, and provides information relevant to their resolution or planned improvement. Much of this annotation is available via our gEVAL browser. However, the track hub allows you to view this annotation in the genome browser of your choice.

The individual tracks currently available are:

  • Genome issues under review by the GRC
  • Genomic regions defined by the GRC
  • Alignments between the primary assembly and alternate loci or patches
  • Clone sequence anomalies
  • Human regions with clones from the CHORI-17 library (CHM1tert)
  • Optical mapping data

In order to attach the track hub

  • specify the following URL to the genome browser: http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt
  • Ensembl: Go to "Add/Manage your data", select "Add your data", then select the data format "TrackHub", and add the hub URL. You need to activate the trackhub tracks under "Configure this page";
  • UCSC Genome Browser: Select the "Track Hubs" button just beneath the main browser area, then select the "My Hubs" tab, and add the hub URL.

More ways of investigating

gEVAL is a genome browser for easy evaluation of genome assemblies, including the most current and not necessarily released versions. It contains the GRC species plus a few others and might help you with your region of interest.

We also provide the ChromoView TPF/AGP viewer for reference genomes and their alternative assembly regions. It shows the current tiling path of sequences and the overlaps between them which are used to make the consensus for each assembly.

Relevant Publications

People

The Genome Reference Informatics Team who forms the Sanger division of the Genome Reference Consortium consists of Senior Bioinformaticians and Senior Computer Biologists to cover software development, data analysis and genome curation.

Name Role
Kerstin Howe SeniorScientific Manager
William Chow Senior Bioinformatician
Joanna Collins Senior Computer Biologist
Sarah Pelan Senior Computer Biologist
Glen Threadgold Computer Biologist
James Torrance Senior Bioinformatician
Jonathan Wood Senior Computer Biologist

Your input

We provide mechanisms by which the scientific community can report loci in need of further review. Information about loci currently under review and genome assembly production cycles are available for human, mouse and zebrafish. More information about the zebrafish genome project can be found here.

* quick link - http://q.sanger.ac.uk/ndm0g928