As the proverbial “fire hose of data” becomes a Niagara torrent, with conservative estimates of 12,000 draft genomes hitting the public databases by 2012, researchers may be surprised to find that these datasets describe genomes that are not complete. Recognizing the problem, a group of researchers from several sequencing centers, including the DOE Joint Genome Institute (JGI), the Sanger Institute and the Human Microbiome Project (HMP) Jumpstart Consortium sequencing institutes, has proposed a new set of standards that expand upon the so-called “Bermuda standard.” In the October 9 issue of the journal Science, they propose four additional categories between “draft” and “finished” status that reflect varying levels of completeness.
“In the past we’ve been limited to two options, requiring us and the other centers to come up with internal definitions,” said DOE JGI metagenomics researcher Patrick Chain at Los Alamos National Laboratory (LANL), first author of the Science paper. “But these are not clear and they’re not propagated to the databases to which we submit sequences. So when users try to download genomes they get data of unknown quality with no information, or a complete genome that they assume has been checked for missing-data errors.”
More on Science Codex.