SALSA: A Domain Specific Architecture for Sequence Alignment

The explosion of genomic data is fostering research in fields such as personalized medicine and agritech, raising the necessity of providing more performant, power-efficient and easy-to-use architectures. Devices such as GPUs and FPGAs, deliver major performance improvements, however, GPUs present notable power consumption, while FPGAs lack programmability. In this paper, we present SALSA, a Domain-Specific Architecture for sequence alignment that is completely configurable, extensible and is based on the RISC-V ISA. SALSA delivers good performance even at 200 MHz, outperforming Rocket, an open-source core, and an Intel Xeon by factors up to 350x in performance and 790x in power efficiency.