RePAIR: A ReRAM-based Processing-in-Memory Accelerator for Indel Realignment

Genomic analysis has attracted a lot of interest recently since it is the key to realizing precision medicine for diseases such as cancer. Among all the genomic analysis pipeline stages, Indel Realignment is the most time-consuming and induces intensive data movements. Thus, we propose RePAIR, the first ReRAM-based processing-in-memory accelerator targeting the Indel Realignment algorithm. To further increase the computation parallelism, we design several mapping and scheduling optimization schemes. RePAIR achieves 7443x speedup and is 27211x more energy efficient over the GATK3.8 running on a CPU server, significantly outperforming the state-of-the-art.