GenMClass: Design and comparative analysis of genome classifier-on-chip platform

We propose GenMClass, a genome classification system-on-chip (SoC) implementing two different classification approaches and comprising two separate classification engines: a DNN accelerator GenDNN, that classifies DNA reads converted to images using a classification neural network, and a similarity search-capable Error Tolerant Content Addressable Memory ETCAM, that classifies genomes by k-mer matching. Classification operations are controlled by an embedded RISCV processor. GenMClass classification platform was designed and manufactured in a commercial 65 nm process. We conduct a comparative analysis of ETCAM and GenDNN classification efficiency as well as their performance, silicon area and power consumption using silicon measurements. The size of GenMClass SoC is 3.4 mm² and its total power consumption (assuming both GenDNN and ETCAM perform classification at the same time) is 144 mW. This allows using GenMClass as a portable classifier for pathogen surveillance during pandemics, food safety and environmental monitoring, agriculture pathogen and antimicrobial resistance control, in the field or at points of care.