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Hybrid-Core Tech Speeds Next-Generation Genomic Sequencing Analysis Pipeline

By BiotechDaily International staff writers
Posted on 05 Mar 2013
A new hybrid-core system increases genomic application performance with lower ownership costs.

Convey Computer (Richardson, TX, USA) announced that the Broad Institute (Cambridge, MA, USA) has installed a Convey HC-2 system as part of their high performance compute farm. The Broad Institute) plans to use the system to speed their genomic pipelines and slash their overall cost of analysis. The Broad Institute is one of the leading biomedical and genomic research centers, generating terabases of sequence data per day.

Convey is working closely with the Broad as they incorporate the Convey system into their pipeline. “We are pleased that the Broad has selected Convey to accelerate critical portions of their next-generation sequencing analysis pipeline,” explained Dr. George Vacek, Director of Convey Computer’s Life Sciences business unit. “Broad is a leader in the adoption of new sequencing technology and in development of corresponding analysis methods. Our ongoing relationship to optimize their analysis tools will have a high impact on researchers worldwide.”

The Broad Institute purchased the Convey system to explore how the hybrid-core computer could accelerate their pipelines while reducing costs. “Although BWA is not a large part of the overall pipeline wall time, in terms of CPU dollars spent it is a very large component,” explained Tim Fennell, director of informatics for the Broad’s genomics platform. “With the Convey system, we expect to increase performance of BWA 10-fold. The Convey system will allow us to increase our efficiency and complete more analysis per dollar.” (The Burrows-Wheeler Aligner [BWA] is an efficient program that aligns comparatively short nucleotide sequences against a long reference sequence such as the human genome.)

Installation of the Convey system at the Broad was quick and easy. “Installing the Convey system was just like installing any other piece of compute hardware. It required no customization at all, fitting naturally into our existing infrastructure,” said Eric Jones, manager of research computing. “Additionally, I’m impressed with Convey’s customer support; I can quickly and easily talk to knowledgeable people.”

Convey’s hybrid-core architecture pairs classic Intel x86 microprocessors with a coprocessor comprised of FPGAs. Particular algorithms—BWA-based alignment, for example—are optimized and translated into code that is loadable onto the coprocessor at runtime. The systems help customers dramatically increase performance over industry standard servers while reducing energy costs associated with high-performance computing.

The world’s first hybrid-core computer, the Convey Computer’s system, combines the low cost and simple programming model of a commodity system with the performance of personalized hardware architecture. Using the Convey hybrid-core systems, users worldwide in industries such as life sciences, research, sophisticated analytics, and the government/defense are appreciating increased application performance and lower costs of ownership.

Related Links:

Convey Computer
Broad Institute



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