In-Storage Read-Centric Seed Location Filtering Using 3D-NAND Flash for Genome Sequence Analysis
Part Of
Proceedings of the Asia and South Pacific Design Automation Conference, ASP-DAC
Start Page
1008
End Page
1015
Date Issued
2025-01-20
Author(s)
You-Kai Zheng
Ming-Liang Wei
Hsiang-Yun Cheng
Ming-Hsiang Tsai
Chia-Chun Chien
Yuan-Hao Zhong
Po-Hao Tseng
Hsiang-Pang Li
Abstract
Read mapping is a critical bottleneck in genome sequence analysis, requiring costly approximate string matching to identify potential matches between reads and a reference genome. Pre-alignment filtering methods aim to mitigate this issue by filtering out unnecessary mapping locations, and implementing them with processing-in-memory (PIM) approaches offers potential benefits by offloading filtering from the computing unit. However, the sparse number of potential mapping locations for each read limits the utilization of PIM's parallel computing capabilities, thereby hindering the overlapping of filtering and sequence alignment to hide filtering latency overheads. In this paper, we propose a 3D NAND-based in-storage pre-alignment filtering approach. Leveraging the read depth property, we introduce a read-centric pre-alignment filtering method that enables parallel comparison of multiple reads. We co-design software and hardware for in-situ processing of read-centric pre-alignment filtering within the storage, capitalizing on 3D NAND Flash's approximate parallel search capability. When integrating with a representative read mapping accelerator, our design achieves an average 1.36x performance improvement with comparable energy consumption. Compared to the state-of-the-art (SOTA) PIM solution, our design results in 123.8x and 53.3x performance gain and energy efficiency improvement.
Event(s)
30th Asia and South Pacific Design Automation Conference, ASP-DAC 2025Tokyo
Publisher
ACM
Type
conference paper