Genomic scientists have been unreservedly enthusiastic about next-gen sequencing. But the seamy underside of these instruments lies in the volume of data they churn out: A single sequencing run can keep a team of bioinformaticists busy for months.
The truth of the matter is, scientists have been sideswiped by their own data. And that couldn’t make bioinformatics firm GenomeQuest any happier. “We have a platform for managing large volumes of sequence data already,” says Ron Ranauro, president and CEO. “We’ve been waiting for the high-speed sequencing market to kick in because that’s what’s going to cause people to rethink their informatics strategies.”
GenomeQuest has been talking to customers to test the theory. One client had been unsuccessful in looking at a sequence file in silico for trace contamination. The problem: the most they could get through in any reasonable period of time was about a quarter of a percent of the data, Ranauro says. “We were able to really get their attention when we could show them on our platform we could exhaustively look at all the sequence reads against all the known reference genomes,” he adds.
Eyeing the growing demand for better analysis tools, GenomeQuest has developed a module specific to short-read data, which is available as a hosted service and can be performed by users in house. Ranauro says the algorithm is platform-independent, so customers can submit fasta files from any next-gen sequencer for analysis.
Instrument vendors, meanwhile, are welcoming this kind of attention for their customers. Applied Biosystems recently launched a service provider program for its SOLiD platform, encouraging other companies to offer analysis solutions. And Tom Jarvie, an application specialist at 454 Life Sciences, says that for cases where customers want more complex analyses than the instrument’s software enables, “that’s where a company like GenomeQuest would be of use to them.”