Enabling Highly-Efficient DNA Sequence Mapping via ReRAM-based TCAM

In the post-pandemic era, third-generation DNA sequencing (TGS) has received increasing attention from both academics and industries. As TGS technologies have become a requisite for extracting DNA sequences, the DNA sequence mapping, which is the most basic bioinformatics application and the core of polymerase chain reaction (PCR) tests, receives great challenges, due to the large size and noisy nature of TGS technologies. In addition, the ever-increasing data volume of DNA sequences also induces the issue of memory wall while large datasets are moved between the memory and the computing units. However, much less effort has been devoted to DNA sequence mapping acceleration while considering both the memory wall issue and the challenges of TGS technologies. To enable highly-efficient DNA sequence mapping, this study proposes a novel resistive random-access memory (ReRAM)-based ternary content-addressable memory (TCAM) and exploits the intrinsic parallelity of ReRAM crossbar for efficient mapping acceleration. Promising results have been demonstrated through a series of experiments with different scales of datasets.