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Brazilian Bioinformatics Institute Taps Convey's Hybrid-Core System for Genomics Research

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Convey Computer said this week that the Brazilian Center for Excellence in Bioinformatics, CEBio, has deployed a Convey HC-1ex hybrid-core computer to handle its genomic data analysis needs.

CEBio is part of the Oswald Cruz Foundation, a scientific institution for research and development in biomedical sciences located in Rio de Janeiro.

According to Guilherme Oliveira, CEBio's coordinator and president of the Brazilian Association for Bioinformatics and Computational Biology, Convey's system will enable CEBio's researchers to speed up their bioinformatics applications; reduce power consumption and costs; and solve computationally intensive problems such as large genome assemblies.

Researchers will use the system to assemble genomes from species like bovine and swine, as well as to handle transcriptomic data analysis, he said.

Prior to purchasing Convey's system, CEBio relied on a 256-node cluster that took too long to complete genomic assemblies, he said.

Convey's hybrid-core architecture pairs Intel x86 microprocessors with a coprocessor comprised of field-programmable gate arrays. It also includes bioinformatics algorithms for DNA sequence mapping and alignment (BI 10/14/2011) and (BI 11/20/2009); and the Convey GraphConstructor which is used to construct and manipulate de Bruijn graphs commonly used in short-read genome assembly applications (BI 5/20/2011).

Additional performance and workflow optimizations include a k-mer counting tool for identifying optimal k-mer length and coverage cutoffs for de novo assembly.

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