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Convey, CLC Bio to Provide Combined Software, Hardware NGS Data-Analysis Solution


By Uduak Grace Thomas

Convey Computer and CLC Bio said this week that they have integrated Convey's hybrid core compute architecture with CLC Bio's Genomics Server and Genomics Workbench solutions.

The combined solution, which allows scientists to run their analysis jobs on Convey's hardware via CLC Bio's software, has already bagged its first customer: the Helmholtz Centre for Infection Research in Braunschweig, Germany, where it is being used to manage and analyze next-generation sequencing data.

HZI researchers explore interactions between bacterial pathogens and their hosts; and strategies to diagnose, prevent, or treat infectious diseases. Specifically, the genome analytics group within HZI provides next-generation sequencing and analysis services to profile genomic, epigenomic, and transcriptomic changes in pathogens and host cells.

Robert Geffers, who heads HZI's genome analytics group, said in a statement that the combined platform provides researchers with "easy-to-use access to the performance" they need to handle the group's large sequencing projects.

The Convey platform, he said, meets HZI's need to run sequencing projects in parallel and process the data with a solution that offers "high performance, compact size, and easy integration with blades we already have."

Convey's hybrid-core architecture pairs classic Intel processors with a coprocessor comprised of field-programmable gate arrays. The company has optimized several bioinformatics algorithms to run on the platform.

These include an accelerated implementation of the Smith-Waterman algorithm (BI 11/20/2009); and a software program called GraphConstructor, launched last May, which speeds up the construction and manipulation of de Bruijn graphs used in short-read genome assembly algorithms such as Velvet and Abyss (BI 5/20/2011).

The company also claims to have a faster version of the Burrows-Wheeler alignment algorithm that increases genome reference mapping rates by a factor of 15 compared to commodity servers (BI 10/14/2011).

For its part, the CLC Bio front end for the Convey system provides HZI researchers with a simple interface and tool suite, whereas "many of our analysis pipelines ... required using a command line and scripts that can be difficult for researchers and clinicians to work with," Geffers said.

He added that the integrated solution is "powerful and provides an excellent user experience," which makes "our researchers much more productive."

Bringing CLC Bio's and Convey's products together was a "pretty straightforward process," Lasse Gorlitz, CLC Bio's director of communications, told BioInform this week.

"The advantage of the Convey platform is that it's sort of a hybrid between [central processing units] and FPGAs," he explained. Since CLC Bio's tools already work well on CPUs, the integration process was "a lot easier than if you wanted to tailor something that was very specific and tied to a single platform."

He explained that the companies have created an interface linking the two systems that allows scientists to set up and run their analysis jobs on the Convey infrastructure — as opposed to their desktop computers — though CLC Bio's software.

The agreement isn't CLC Bio's first partnership with a hardware firm. The company announced earlier this year that it was integrating its server and desktop-based sequence analysis software tools with SciEngines' FPGA-based platform dubbed Rivyera, which would offer implementations of Blastn, Blastp, and the Smith-Waterman algorithm, with other algorithms added later (BI 1/13/2012).

Last year, CLC Bio competitor Biomatters launched a similar strategy by partnering with ActiveMotif's TimeLogic to allow users of its Geneious Server software to run bioinformatics jobs on Time Logic's FPGA-based DeCypher system (BI 1/14/2012).

Gorlitz noted that CLC Bio's strategy is to form multiple partnerships with different hardware companies — much the same way its software supports several sequencing platforms.

"If [a company] wants to partner and they are able to leverage that partnership so that it makes sense for us to invest some resources in it, then we are absolutely interested in investigating most opportunities," he said.

"We really ... focus on the strengths of the individual companies participating in the collaboration," he added. "Convey is a very well-established company already and we had and still have a very positive work environment with them so it's been a very good project for us."

In a statement, George Vacek, director of Convey Computer's life sciences business unit, said that the company is "pleased" to partner with CLC Bio for customers like HZI.

He told BioInform that his firm expects to continue to provide the combined solution to other customers in the genomics space.

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.