After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000002035.4/). This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. GRCz11 shows a significant reduction in scaffold numbers and increase in scaffold N50 whilst the overall genome size was not affected. For the first time in a zebrafish assembly, GRCz11 also features alternate loci scaffolds (ALT_REF_LOCI) for representations of variant sequences. The alignments of the alternate loci scaffolds to the primary chromosomal path are also included in the GRCz11 assembly to provide the chromosome context for these alternate sequences.
For more details, please have a look at http://genomeref.blogspot.co.uk/2017/05/grcz11-latest-zebrafish-reference.html