System-on-Chip Lab (SoCL)

Seminar: Analyzing Genomes via Efficient HW/SW Co-Design

February 9, 2022

Speaker: Dr. Mohammed Alser, a Senior Researcher and Lecturer of Bioinformatics and Computer Architecture at ETH Zurich.

Brief: Our understanding of human genomes today is affected by the ability of modern computing technology to quickly and accurately determine an individual’s entire genome. Analyzing our genomes is the foundation of many scientific and medical discoveries, and serves as a key enabler of personalized medicine.

Our starting axiom for a modern genome analysis is that it should interpret our genomes accurately, quickly, and affordably enough. This talk describes our ongoing journey in enabling efficient genome analysis. We first provide a brief background on computational methods that can comprehensively find variations in genomes and tolerate sequencing errors. Then, we describe our new algorithmic methods and hardware-based acceleration approaches.

Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or new execution paradigms, like processing in memory.

We show that significant improvements are possible with algorithmic methods, hardware accelerators, and their combination. We demonstrate how our new algorithms provide very fast and accurate analysis of microbial genomes. We conclude with a foreshadowing of future challenges and research directions triggered by the development of very low cost yet highly error-prone new sequencing technologies.

View seminar here.