Tsai, Ming-HsiangMing-HsiangTsaiWei, Ming-LiangMing-LiangWeiChien, Chia-ChunChia-ChunChienTseng, Po-HaoPo-HaoTsengLee, Yung-ChunYung-ChunLeeLi, Hsiang-PangHsiang-PangLiYang, Chia-LinChia-LinYang2026-04-162026-04-162025-11-2010923152https://www.scopus.com/record/display.uri?eid=2-s2.0-105029428926&origin=resultslisthttps://scholars.lib.ntu.edu.tw/handle/123456789/737225Genomic 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.falseExact match filterGenomic alignmentGroup testingPre-alignment filterconference paper10.1109/iccad66269.2025.112408792-s2.0-105029428926