GCOC: A Genome Classifier-On-Chip based on Similarity Search Content Addressable Memory.

GCOC is a genome classification system-on-chip (SoC) that classifies genomes by k-mer matching, an approach that divides a DNA query sequence into a set of short DNA fragments of size k, which are searched in a reference genome database, with the underlying assumption that sequenced DNA reads of the same organism (or its close variants) share most of such k-mers. At the core of GCOC is a similarity, or approximate search-capable Content Addressable Memory (SAS-CAM), which in addition to exact match, also supports approximate, or Hamming distance tolerant search. Classification operation is controlled by an embedded RISC-V processor.