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CLC bio A/S. (7/9/13). "Press Release: CLC bio and SciEngines Enable Real-time Exact Alignment of NGS Data with Accelerated Sequence Alignment Solution". Kiel & Aarhus.

Organisations Organisation CLC bio A/S
  Today Qiagen Aarhus A/S
  Group Qiagen (Group)
  Organisation 2 SciEngines GmbH
Products Product CLC Genomics Workbench
  Product 2 server
Index term Index term CLC bio–SciEngines: bioinformatics, 201307 collab integration of CLC sequence analysis s/w with SciEngines Rivyera computers
Person Person Görlitz, Lasse (CLC bio 2010109 Director of Communications)

As a result of their ongoing partnership, CLC bio and SciEngines today announced an integration between CLC bio's sequence analysis software and the newest model of SciEngines' FPGA-based RIVYERA computers. Instead of using heuristics, it is now possible to find exact matches between sequences at a speed of 11.5 trillion cell updates per second (CUPS) per server, approximately 3000x faster than a 3.0 GHz CPU thread.

In cases, where the scientist requires highest possible analysis quality but where ordinary computers are simply too slow, our RIVYERA architecture is opening up completely new possibilities. With the newest features in our Smith-Waterman implementation, the speed of the RIVYERA S6-LX150 and the intuitive usability of CLC bio's front-end, we're confident that exact sequence alignment approaches executed in real-time will start to play an increasing role in modern computational biology.

Vice President at SciEngines, Tim Pietruck
"In addition to the speed, we're confident our customers will gain tremendous value from the full-fledged feature set, including user-definable scoring matrices, support of affine gap penalties, reverse complement calculation, and mate-pair alignments. We're looking forward to see what compelling results our customers and partners potentially can achieve with this system!."

VP of Communications, Lasse Görlitz
"The combined solution is now available in a beta version, which will be demonstrated at the ISMB/ECCB conference in Berlin, Germany, July 21-23, 2013."


The performance benchmark has been executed on a RIVYERA S6-LX150 computer with 256 FPGAs. The dataset consisted of 2.480.868 reads, each with 100 basepairs length plus the reverse complement and was retrieved from 1000 genomes project NA12878. The dataset was aligned with hg19 chromosome 6 (171 million basepairs in size) and the unix time command used to calculate overall user-time. With a runtime of close to 1 hour (3591 seconds), this results in a performance of 11.8 trillion cell updates per second (TCUPS), which signifies close to 3000x higher performance than a 3.0 GHz Xeon thread, replacing a full rack of commodity servers.

About SciEngines

About CLC bio

Contact SciEngines

Tim Pietruck, Vice-President Customer Solutions
Phone: +49 (431) 530 2482
Contact CLC bio

Lasse Görlitz, VP of Communications
Tel: +1 (617) 765 0687

Record changed: 2017-04-02


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