Speaker: Dr. Zhenman Fang, Ph.D.,
IDRE Scholar,
Computer Science Department,
University of California, Los Angeles

Time: 11:45 A.M. – 1 P.M. (Lunch will be serverd*)
Date: Apr 12, 2017
Location: 5628, Math Sciences Building
RSVP: https://idre.ucla.edu/calendar-event/accel-next-gen-dna-seqn#rsvp

Abstract: Modern medical research is being transformed with the advance of next-generation sequencing technologies that dramatically reduce the cost of sequencing an individual human genome from $10M to $1,000 in the past decade. This sequencing technology is widely utilized in research and is transitioning into the clinic for applications such as sequencing cancer tumors. To be more cost-effective, genome sequencers obtain the sequence of billions of small fragments in the range of a few hundred nucleotides (called short reads) of a whole genome. Therefore, we have to reconstruct all these short reads back into a whole human genome for genome variant calling and cancer discovery. This poses great computational challenges: state-of-the-art DNA sequencing pipeline takes around a week on a 12-core CPU server.

In this talk, I will present various ways to accelerate the next-generation DNA sequencing pipeline done in our Center for Domain-Specific Computing (CDSC), with the final goal to reduce the computation time to a few hours. First, we scale out the computation by leveraging the power of a CPU cluster/datacenter. Second, we scale up the computation by developing hardware accelerators on commodity energy-efficient FPGAs that can be plugged into the CPU server. Moreover, we combine these two techniques and address the new challenges in FPGA-enabled datacenters. I will talk about our current status in accelerating the DNA sequencing pipeline and show some promising results we have achieved using the aforementioned techniques [FCCM 2015, HotCloud 2016, ACM SOCC 2016].