JGI Finishing Policy
Prokaryote Projects
The JGI will attempt to finish the genome sequence for all prokaryote projects. Finishing commences after the completion of draft sequencing. It involves the identification and resolution of misassemblies and repeat regions, gap closure, and improvement of low-quality regions. In addition to the automated annotation of the draft sequence, the finished genome will be sent to Oak Ridge National Laboratory for one additional round of automatic annotation. If the genome is finished before the expiration of the six-month period of exclusive collaborator access, the collaborator will also be given exclusive access to the finished genome and all annotations until the data are submitted to GenBank.
JGI Prokaryote Finishing Standards
- All low-quality areas (<Q30) are reviewed and resequenced.
- The final error rate must be less than 0.2 per 10 Kb.
- No single-clone coverage is permitted (minimum of 2x depth everywhere).
- Single-stranded regions are manually inspected and quantified.
- All positions where an aligned high-quality read (>Q29) disagrees with the consensus base are checked.
- All strings of xxxx are resolved in the final sequence.
- All repeats are verified.
- The ends of final contigs (chromosomes, plasmids) are checked
- The final assembly is given a manual QC check.
If finishing is not completed within twelve months of the completion of the draft assembly, then the latest assembly of the enhanced project (i.e., the project with improvements made thus far) will be annotated and submitted to GenBank. No further finishing efforts will be made.
Eukaryote projects
At the time of approval, eukaryotic projects at the JGI are expected to produce a draft genome. Projects are prioritized for further genome improvement based upon DOE mission relevance and feasibility for the finishing genome.
