MeG2: In-Memory Acceleration for Genome Graphs Analysis

Genome graphs analysis has emerged as an effective means to enable mapping DNA fragments (known as reads) to the reference genome. It replaces the traditional linear reference with a graph-based representation to augment the genetic variations and diversity information, significantly improving the quality of genotyping. The in-depth characterization of genome graphs analysis uncovers that it is bottlenecked by the irregular seed index access and the intensive alignment operation, stressing both the memory system and computing resources.Based on these observations, we propose MeG2, a lightweight, commodity DRAM-compliant, processing-in-memory architecture to accelerate genome graphs analysis. MeG2is specifically integrated with the capabilities of both near-memory processing and bitwise in-situ computation. Specifically, MeG2leverages the low access latency of near-memory processing with the index-centric offload mechanism to alleviate the irregular memory access in the seeding procedure, and harnesses the row-parallel capacity of in-situ computation with the distance-aware technique to exploit the intensive computational parallelism in the alignment process. Results show that MeG2outperforms the CPU-, GPU-, and ASIC-based genome graphs analysis solutions by 502× (30.2×), 272× (15.1× ), and 5.5× (8.3×) for short (long) reads, while reducing energy consumption by 1628× (85.6×), 1443× (77.1×), and 7.8× (11.7×), respectively. We also demonstrate that MeG2offers significant improvements over existing PIM-based genome sequence analysis accelerators.