Zebrafish (GRCz11)
Danio_rerio - Genome Reference Consortium
The zebrafish genome project is a collaboration between the Sanger Institute and the zebrafish community, announced during the Sanger Institute Zebrafish Workshop 2000 and was started in February 2001.
GRCz11 is the next iteration of the major release of the reference assembly of zebrafish, the last being GRCz10 in 2014. GRCz11 has been refined by the addition of nearly 1000 finished clone sequences and increased contiguity by leveraging various datasets such as Bionano optical maps. This has led to the resolution of more than 400 assembly issues and increased scaffold N50 by 3.4X as compared to GRCz10.
The other major addition to GRCz11 is the representation of alternate loci scaffolds (ALT_REF_LOCI), similar to those seen in the Human and Mouse Reference GRC projects. More can be read here.
GRCz11 genome assembly record details can be found here: GCA_000002035.4.
GRC will remain the caretaker of the zebrafish reference assembly, but curation will now be transferred from the Sanger team to GRC's newest member ZFIN. However, gEVAL activities surrounding zebrafish assemblies will continue.
Manual annotation of this genome can be found in
Vega
View karyotype
Example region
More information and statistics (N50, Coverage, BUSCO)
Retrieve a live status of the current tiling path using the tool Chromoview
Display your data in gEVAL
Punchlist OverviewPunchlists
The Zebrafish Punchlists are automated lists created to facilitate identification of and navigation to common issues or regions of interest.
Examples include:
- Gap Locations
- Overlap Issues
- Clone Spanning Locations
If you would like to recommend a punchlist to be added to a specific organism or in general please contact us
Example Jira TicketThe Genome Reference Consortium
The Zebrafish gEVAL is maintained and improved by the Genome Reference Consortium (GRC)
Jira Ticketing System: Jira is the ticketing tracking system used by the GRC for genome issues. This can be a gap, path, variation, gene or other issues submitted by external users
Comparative genomics
gEVAL provides intra-species alignments. This is available for intermediate builds, major reference releases, and WGS/NGS assemblies.