Zebrafish Genome Project

The Sanger Insitute started the zebrafish genome sequencing project in 2001 and has generated several genome assemblies. After the release of Zv9, the zebrafish genome project joined the Genome Reference Consortium (GRC) for further improvement and ongoing maintenance. The GRC has now released a new reference assembly, GRCz10

It will take a while until the genome browsers like Ensembl update to GRCz10. In the meantime, Zv9 is being featured. You can view the regions that have been addressed by the GRC in Ensembl by attaching the 'GRC regions Zv9' DAS source. Simply click here.

Email us at zfish-help@sanger.ac.uk with your comments and enquiries, your input is welcome!

Frequently asked questions are answered here.

Genome Publication
The zebrafish reference genome sequence and its relationship to the human genome
Kerstin Howe, Matthew D. Clark et al.
Nature (2013);496(7446):498-503.
PUBMED: 23594743, PMCID: PMC3703927, DOI: 10.1038/nature12111

[Wellcome Library, London]

  • Resources
  • News
  • Frequently asked questions

Browsers Featuring Current Clone Path Data

  • gEVAL (Genome Assembly Evaluation browser) - Browse the latest clone path and evaluate overlaps, contig order/orientation and aligment with supporting data.
  • Chomoview (Assembly Browser) - Access the daily updated zebrafish clone path: search for clones with their accession or name, browse the paths and download the sequences.

Search Sequence Data

  • Blast against all zebrafish clone sequences and two nextgen assemblies
  • Status of a clone in the sequencing pipeline
  • Details about clone libraries
  • Online RepeatMasker

Download Data

  • Download assemblies and assembly information
  • Download clone sequence files

Genome Annotation on the Latest Assembly Zv9

  • Zebrafish Ensembl - Access to the annotated zebrafish genome from the latest Ensembl assembly.
  • Zebrafish Vega - Browse manually annotated zebrafish genome sequences from which data, assemblies and annotation are released frequently.

Tutorials

  • Material from the Zebrafish Web Resources Workshop, Madison 2014
  • 17.09.2014:

    New zebrafish reference genome GRCz10 released

    The genome Reference Consortium released has released an improved version of the zebrafish genome assembly, GRCz10. Details can be found here

  • 03.07.2014:

    Opendoor Workshop at 11th International Meeting on Zebrafish Development and Genetics 2014: Working with Zebrafish Genome Resources

    The workshop manuals and presentations are now available for download at the workshop website.

  • 20.12.2013:

    Opendoor Workshop at 11th International Meeting on Zebrafish Development and Genetics 2014: Working with Zebrafish Genome Resources

    In association with ZFIN and the NCBI, the Wellcome Trust Sanger Institute are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop on June 24th, 2014). Registration will open on February 25th, 2014 at the official conference website.

  • 11.12.2013:

    Zebrafish Genome Paper Published

    Nature published a corrigendum to the zebrafish genome paper to update the author list.

  • 17.04.2013:

    Zebrafish Genome Paper Published

    The paper describing the zebrafish genome sequence and its relationship to the human genome has been published. If you are interested in the sequence details, make sure to have a look at the supplementary material.

  • 21.02.2013:

    Opendoor Workshop at 8th European Zebrafish Meeting, Barcelona, 2013: Working with Zebrafish Genome Resources

    In association with the 8th European Zebrafish Meeting, the Wellcome Trust Sanger Institute are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop (The workshop will run from 10:00 - 18:00 on Tuesday 9th July). Each workshop is broken into modules designed to give a broad overview of a given topic with examples chosen by the trainers. The modular structure consists of a discussion of theory and methods, coverage of software and web resources, and a series of "hands on" worked examples. Time is provided in each session for participants to carry out their own research in the presence of the trainers, and participants are encouraged to bring their own problems (e.g sequence for analysis) with them. All materials used during the workshop series will be available on the Web, in the form of manuals and information. Zebrafish specific examples will be used wherever possible.

    Please visit our website for further details and on-line registration. Any queries should be sent to zebrafish-odw@sanger.ac.uk.

Related Links

  • Projects
  • Academic Faculty
  • Mouse resources
  • Cancer genome project
  • Genome reference consortium
  • The Genome Campus
  • What we do
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