MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
Melina Soysal, Konstantina Koliogeorgi, Can Fırtına, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco de Oliveira Junior, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, Onur Mutlu · 2025
Conventional genome analysis relies on translating the noisy raw electrical signals generated by DNA sequencing technologies into nucleotide bases (i.e., A, C, G, and T) through a computationally-intensive process called basecalling.Raw signal genome analysis (RSGA) has emerged as a promising approach towards enabling real-time genome analysis by directly analyzing raw electrical signals without the need for basecalling.However, rapid advancements in sequencing technologies make it increasingly difficult for softwarebased RSGA to match the throughput of raw signal generation.Hardware-based RSGA acceleration has the potential to bridge the gap between software-based RSGA and sequencing throughput.