Accelerating Genome Alignment Pipeline with In-NAND Search Technology and Group Testing Techniques
Journal
IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD
Start Page
1
End Page
10
ISSN
10923152
ISBN (of the container)
979-833151560-7
Date Issued
2025-11-20
Author(s)
Tsai, Ming-Hsiang
Wei, Ming-Liang
Chien, Chia-Chun
Tseng, Po-Hao
Lee, Yung-Chun
Li, Hsiang-Pang
Abstract
Genomic sequence analysis deciphers and interprets an organism's DNA, offering crucial insights into personalized medicine, disease diagnosis, evolutionary biology, and agricultural biotechnology. While Next-Generation Sequencing (NGS) has revolutionized genomics by providing a fast and cost-effective method for generating genomic sequences, the computational complexity of aligning short reads back to a reference genome remains a significant bottleneck. The exact-match-based preseeding filter has emerged as an effective and general methodology to address this issue, capable of removing 70% to 80% of exact-matched genomic reads at the source and applicable to a wide range of alignment tools. However, the state-of-the-art exact-match filter architecture, GenStore, encounters performance limitations due to the need to load reference sequences from NAND flash memory to the controller page by page.In this work, we propose a novel Solid-State Drive (SSD) architecture that leverages computing-in-NAND-flash techniques to perform match detection directly within memory. By harnessing the two-dimensional input capability of 3D NAND flash memory and integrating group testing methods, our design enables comparisons across hundreds of pages in a single read cycle and supports simultaneous multi-query searches. Combined with a Bloom filter for in-NAND search, our architecture significantly reduces data movement by 48% to 96%, achieves a speedup of 1.60× to 4.99× over GenStore, and delivers 30% higher energy efficiency with only a 4.5% circuit overhead.
Event(s)
44th IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2025
Subjects
Exact match filter
Genomic alignment
Group testing
Pre-alignment filter
Publisher
Institute of Electrical and Electronics Engineers Inc.
Type
conference paper