Sequencing Strategy
The JGI performs standard Sanger sequencing at its Production Genomics Facility in Walnut Creek, California. The process for most genomes employs the whole-genome shotgun sequencing method to produce high-quality draft sequence. The work begins with creation of 3-Kb, 8-Kb, and 40-Kb DNA libraries. We sequence from both sides of the library insert, producing paired ends, typically resulting in approximately 8-9X depth. For all large genome projects, sequenced reads are deposited in the GenBank Trace Archive at NCBI. Reads are aligned by using various genome assemblers to produce the primary draft assembly, which consists of contigs linked into larger scaffolds by paired-end information. The PGF and several partner institutions--Stanford University, Los Alamos National Laboratory, and Lawrence Livermore National Laboratory--perform finishing work (gap closing, quality improvement, and assembly verification) for organisms that require this level of refinement. All genomes have at least a minimal automated annotation, and most may be searched on genome browsers via the Genome Portal.
