ReTAP: Processing-in-ReRAM Bitap Approximate String Matching Accelerator for Genomic Analysis

Tsung Yu Liu, Yen An Lu, James Yu, Chin Fu Nien*, Hsiang Yun Cheng*

*此作品的通信作者

研究成果: Conference contribution同行評審

摘要

Read mapping, which involves computationally in-tensive approximate string matching (ASM) on large datasets, is the primary performance bottleneck in genome sequence analysis. To accelerate read mapping, a processing-in-memory (PIM) architecture that conducts highly parallel computations within the memory to reduce energy-inefficient data movements can be a promising solution. In this paper, we present ReTAP, a processing-in-ReRAM Bitap accelerator for genomic analysis. Instead of using the intricate dynamic programming algorithm, our design incorporates the Bitap algorithm, which uses only simple bitwise operations to perform ASM. Additionally, we explore the opportunity to reduce redundant computations by dynamically adjusting the error tolerance of Bitap and co-design the hardware to enhance computation parallelism. Our evaluation demonstrates that ReTAP outperforms GenASM, the state-of-the-art Bitap accelerator, with a 153.7 x higher throughput.

原文English
主出版物標題2024 Design, Automation and Test in Europe Conference and Exhibition, DATE 2024 - Proceedings
發行者Institute of Electrical and Electronics Engineers Inc.
ISBN(電子)9798350348590
出版狀態Published - 2024
事件2024 Design, Automation and Test in Europe Conference and Exhibition, DATE 2024 - Valencia, 西班牙
持續時間: 25 3月 202427 3月 2024

出版系列

名字Proceedings -Design, Automation and Test in Europe, DATE
ISSN(列印)1530-1591

Conference

Conference2024 Design, Automation and Test in Europe Conference and Exhibition, DATE 2024
國家/地區西班牙
城市Valencia
期間25/03/2427/03/24

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