New zebrafish genome reference assembly GRCz10 now available

[Williams, Jason (SOP)]

Hello, I am a Graduate Student at the University of Colorado Denver. I use UCSC Genome browser quite often and I was curious when the new Zv10 will be incorporated into your site.

Thank you,

Jason Williams

Graduate Student
University of Colorado Denver
Anschutz Medical Campus
Cell Biology, Stem Cells, and Development
Kristin Artinger lab
303.724.4563

From: zfinadmn <jkn...@cs.uoregon.edu>
Date: September 19, 2014 at 10:59:38 AM MDT
To: <zfin...@lists.uoregon.edu>
Subject: [Zfin_list] New zebrafish genome reference assembly GRCz10 now available
Reply-To: <zfin...@zfin.org>

The GRC announces the release of GRCz10. GRCz10 is the first zebrafish reference assembly produced by the GRC and replaces Zv9.

This is a major, coordinate changing, assembly release.

 

The assembly files can be retrieved from either the new or old GenBank FTP site:

New: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_other/Danio_rerio/all_assembly_versions/GCA_000002035.3_GRCz10/

Old: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/GRCz10

 

A summary of new features in GRCz10 is provided in the GRC blog post: “GRCz10 - The GRC's first zebrafish genome reference assembly”:http://genomeref.blogspot.com/

 

We welcome your feedback. Please write to us at zfish...@sanger.ac.uk or use the form available at http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/contact.shtml

Best wishes,

Kerstin Howe on behalf of the Genome Reference Consortium 

[Jonathan Casper]

Hello Jason,

Thank you for your question about the availability of the Zv10 genome assembly. We have plans to add this assembly to our browser and it does have a high priority for us, but we do not yet have a timetable for when it will be ready. Prior to release, a test browser will go up at http://genome-test.soe.ucsc.edu. You are welcome to use the test browser when it becomes available, with the proviso that it is still a test server: much of the data will not have gone through our quality review process and may be subject to change.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

--