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Swamped in Sequence Data? Consed Developer Says Autofinish Could Speed Completion

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Interest in automated finishing techniques for shotgun sequence data has certainly increased in recent months, according to David Gordon, co-author of the Autofinish program that is part of the University of Washington’s Consed package.

Gordon said the program is “getting more and more known” as labs scramble to boost their finishing rates to match automated sequencing rates.

Since most finishing decisions, such as which directed reads to obtain, are still made by people, many labs have found that the gap between sequenced and finished data has widened as automated sequencers pump out data at an ever-increasing rate. Gordon and his colleagues designed Autofinish to automatically suggest the optimum finishing reads for closing the gaps in a sequencing project.

“The thing that makes Auto- finish unique is that it provides objective criteria to guide the finishing process rather than having ad hoc rules,” said Gordon. “You set a target error rate and it will finish to achieve that target error rate, trying to minimize the cost in doing so.”

Gordon said he’s not aware of any other automated software tools that use the objective criteria of error probabilities to guide the selection process.

Gordon, along with the University of Washington’s Phil Green and Cindy Desmarais, recently published a paper in Genome Research detailing a comparison between a human finisher and an Autofinish/human hybrid approach for five different sequencing projects. While the Autofinish-hybrid and the human finisher required roughly the same number and type of reads, the Autofinish-hybrid completed the five sequencing projects in 17.8 hours compared to 48.2 hours for the human finisher alone.

While labs could save a great deal of time using Autofinish, Gordon cautions that it does not yet completely automate the finishing process. He recommends that Autofinish be used for three rounds completely automatically with no human intervention. After the three rounds, a human finisher should check if there is still any further manual work that needs to be done.

As part of the Consed package, Autofinish is available for free to academic labs and may be licensed by commercial entities for $2,500 per site, regardless of the number of users or computers.

“Clearly we’re not in it for the money,” said Gordon. “The reason that we sell it at all is because that money supports further development of Consed and Autofinish.”

Consed and Autofinish are currently licensed by around 900 sites in 36 countries. Current users include the Genome Sequencing Center at Washington University, the Department of Energy Joint Genome Microbial Project, The Berkeley Drosophila Genome Project at Lawrence Berkeley National Laboratory, and a number of other private and public labs.

— BT

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