DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

Abstract

ABSTRACTWe propose a novel dynamic storage-based approximate search content addressable memory (DASH-CAM) for computational genomics applications, particularly for identification and classification of viral pathogens of epidemic significance. DASH-CAM provides 5.5× better density compared to state-of-the-art SRAM-based approximate search CAM. This allows using DASH-CAM as a portable classifier that can be applied to pathogen surveillance in low-quality field settings during pandemics, as well as to pathogen diagnostics at points of care. DASH-CAM approximate search capabilities allow a high level of flexibility when dealing with a variety of industrial sequencers with different error profiles. DASH-CAM achieves up to 30% and 20% higherF1score when classifying DNA reads with 10% error rate, compared to state-of-the-art DNA classification tools MetaCache-GPU and Kraken2 respectively. Simulated at 1GHz, DASH-CAM provides 1, 178× and 1, 040× average speedup over MetaCache-GPU and Kraken2 respectively.CCS CONCEPTS•Hardware→Bio-embedded electronics.