Biology Needs Computer Architects: Keeping Up with Genomic-scale Data

Speaker: Sneha Goenka, PhD Student, Stanford University
Date: June 14, 2023

The landscape of computing has undergone a significant transformation with the death of Dennard scaling and the slowing of Moore’s law: applications now drive innovations in computer systems architecture. At the same time, the advent of high throughput, low cost sequencing technology has revolutionized genomics. The massive amount of data generated in genomics has uncovered acute compute challenges in biological inference due to limitations of software on traditional multi-core systems. To address this challenge, my research employs a hardware-software-algorithm co-design approach to significantly improve computational performance in key areas of comparative and clinical genomics.

In this talk, I will present systems that accelerate pipelines in both these domains of genomics. First, I will present Darwin-WGA (FPGA/ASIC) and SegAlign (GPU) for cross-species whole genome alignment where co-design has yielded orders of magnitude increase in speed. Additionally, there are gains in accuracy while modifying the algorithm to improve the underlying hardware implementation. Next, I will talk about the ultra-rapid nanopore whole genome sequencing pipeline that can deliver a genetic diagnosis in under 8 hours, making it the fastest pipeline to date. The scalable, cloud-based distributed infrastructure overcomes system bottlenecks to enable near real-time computation and improved variant identification. This pipeline has been deployed in critical care units in Stanford hospitals and applied to 13 patients. Finally, I will share my vision for continued advancements in computer systems applied to emerging fields such as pangenomics, single cell genomics, and long read clinical sequencing.