The Fugu v.3.0 (Aug. 2002) whole genome shotgun assembly was provided by the US DOE Joint Genome Institute (JGI). The assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are plasmid, cosmid, or BAC end sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 20,379 scaffolds totaling 319 million base pairs. The largest 679 scaffolds total 160 million base pairs.
The alignments were done with blat in translated protein mode requiring two nearby 4-mer matches to trigger a detailed alignment. The human genome was masked with RepeatMasker and Tandem Repeat Finder before running blat.
The 3.0 draft from the JGI Fugu rubripes website was used in the UCSC Genome Browser Fugu blat alignments. These data have been provided freely by the JGI for use in this publication only.