The whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired end sequencing reads at a coverage of 5.7X produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage coming from 2 kb insert plasmids. The assembly contains 8,597 scaffolds totaling 319 million base pairs; the largest 679 scaffolds total 160 million base pairs. Gene modeling and analysis were performed at JGI, Singapore, Cambridge, and the Institute for Systems Biology.
The alignments were done with BLAT in translated protein mode requiring 2 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 http://genome.jgi-psf.org/fugu6/fugu6.info.html was used in the UCSC fugu BLAT alignments.