CiMBA: Accelerating Genome Sequencing Through On-Device Basecalling via Compute-in-Memory

Apr 9, 2025 by W. Simon, I. Boybat, Riselda Kodra, E. Ferro, Gagandeep Singh, M. Alser, Shubham Jain, H. Tsai, Geoffrey W. Burr, O. Mutlu, A. Sebastian (IEEE Transactions on Parallel and Distributed Systems)

As genome sequencing is finding utility in a wide variety of domains beyond the confines of traditional medical settings, its computational pipeline faces two significant challenges. First, the creation of up to 0.5 GB of data per minute imposes substantial communication and storage overheads. Second, the sequencing pipeline is bottlenecked at the basecalling step, consuming >40% of genome analysis time.