Data analysis on demand

GenomeQuest rolls out next-gen sequencing research platform

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WESTBOROUGH, Mass.—Seeking to shorten the lead time between sequencer output and assembled and annotated scientific information for its genomics research customers, GenomeQuest Inc. has launched On-Demand Informatics, a Web-based application that allows scientists to access massive bioinformatics resources the day after a sequencing run completes.

"In this evolution of what is referred to as next-generation sequencing, absolutely enormous volumes of data are being produced," says Ronald Ranauro, president and CEO of GenomeQuest. "We talked to our customers, and they said processing and data management challenges are beyond the limits of all but some of the largest genome centers. Next-generation sequencing is informative, but is not going to happen overnight. The notion was to add to our system the components that would make it a platform for mining and managing next-generation sequencing data and allowing biologists to gain insight."

On-Demand Informatics allows researchers to securely access GenomeQuest's bio-medical compute cloud resources to turn raw next-gen sequencing data into queryable sequence databases for further Web-based analysis.

Applications enabled by the solution include in-silico purification of next-generation sequencing samples, transcript discovery, gene expression and gene regulation and variant detection studies. Final data can be output into statistical reports or downloaded into a range of third-party software tools.

The solution can significantly shrink the 12 to 18 months a next-generation sequencing study typically faces, Ranauro says.

"On-Demand gives a researcher access to large-scale bioinformatics expertise from any Web browser and the ability to turn raw sequencing data into something that is eminently more useful," he says.

On-Demand was a huge draw for Dr. Maher Al Rwahnih, a researcher with the University of California's Department of Plant Pathology, who is using the solution in research involving unknown viruses.

 "With On-Demand, we can just type in a search string and it does the filtering for us—with programs like Excel, we have to go through data line by line," Al Rwahnih says. "There is also no way we have the memory needed to store this data, so the Web-based function is critical. In addition, for us one of the most important benefits is eliminating the need for us to hire outside people to do the sequencing for us. I am a biologist first, and then I have a very basic knowledge of computing. All of this impacts our research in a very positive way." DDN

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