map, clones and Vega

frequently asked questions

Zebrafish genome assemblies

The integrated zebrafish genome assembly is created by filling the remaining gaps in the clone path with whole genome shotgun (WGS) contigs.

The most recent whole genome shotgun assembly, WGS31, has been created using Illumina sequencing reads from a double-haploid Tübingen fish (289 million reads providing approximately 30-fold coverage), combined with capillary sequencing reads from a second related double-haploid Tuebingen fish (12.2 million reads providing approximately 7.5-fold coverage). This use of data from double-haploid Tuebingen fish results in less artificial haplotypic duplication than was found in previous WGS assemblies which were generated from multiple individual diploid fish. A novel de Bruijn graph based algorithm called Fuzzypath was used to assemble the Illumina reads into short sequence contigs; these contigs were then combined with the capillary reads using the Phusion assembler.

Earlier WGS assemblies were based on DNA sequence from ~1000 zebrafish embryos. The resulting reads were assembled with Phusion. From Zv5 onwards, WGS assemblies included reads from a single Tübingen, double haploid zebrafish.

		Pre-ensembl Pre-ensembl currently features the most recent assembly, Zv9. Zv9 in pre-ensembl ftp download information Ensembl Ensembl currently features the previous Zv8 assembly complete with gene build and comparative genomics data. DAS sources can be added to the browser to view additional data aligned to the genome assembly Zv8 based zebrafish Ensembl search the assembly with Blast/SSAHA DAS sources community annotation ftp download information Previous assemblies seventh assembly Zv7 ftp download information sixth assembly Zv6 ftp download information fifth assembly Zv5 Ensembl archive ftp download information fourth assembly Zv4 Ensembl archive ftp download information third assembly Zv3 ftp download information second assembly Zv2 ftp download information first assembly Zv1 ftp download information Other DAS Server Frequently asked questions