Monday, June 8, 2020

ZFIN and the GRC: Supporting the zebrafish reference genome assembly


ZFIN is a member of The Genome Reference Consortium (GRC), an international collaboration consisting of NCBI, the Wellcome Trust Sanger Institute, the McDonnell Genome Institute at Washington University, the European Bioinformatics Institute (EBI) and ZFIN. This consortium is tasked with ensuring that the reference assemblies for human, mouse, zebrafish and chicken are updated and improved through new data and analysis from genome centers and the research community.

The zebrafish-specific GRC webpage (Fig. 1) provides an overview of the zebrafish genome, including an ideogram of the latest zebrafish assembly (GRCz11) that highlights the location of alternate loci scaffolds, downloadable files for the current public assemby and the tiling path files reflecting the latest assembly edits, as well as links to genome assembly data and genome regions under review. Zebrafish genome issues (Fig. 2), such as sequencing errors, gaps, and path problems, can be browsed at the chromosome level, filtered by problem type or status or searched by gene, location, clone name or accession.

If you come across what you suspect is a problem in the build in the course of your research, visit the GRC website to search the list of genome issues and if it has yet to be reported, select the "Report an Issue" tab in the header (Fig. 3) to report information about the potential problem in the build. Be as complete as possible and provide location, flanking sequences and a description of the issue. Genome annotators will evaluate the region, determine if an update to the genome is needed and submit data to create a new tiling path to improve the build with an update or "patch".

We welcome your feedback!

Figure 1 Zebrafish specific GRC webpage
Figure 1

Figure 2 Zebrafish genome issues webpage
Figure 2

Figure 3 Report a Genome Problem webpage
Figure 3

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