iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing

doi:10.1007/s11390-025-5022-y

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	iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing
	Liu, Wan-Qi 1; Li, Ye-Wen 3; Tan, Guang-Min 1,2
	2026-01-21
发表期刊	JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
ISSN	1000-9000
页码	18
摘要	With the rapid expansion of genomic sequencing data over the years, the costs associated with storage, transmission, and bandwidth are becoming the primary bottlenecks in genomic research and applications. Data compression is widely used to alleviate this burden, provided it achieves a sufficiently high compression ratio and fast compression speed. MPEG-G is a genome-specific compression standard that offers a higher compression ratio than general-purpose compression tools (4.3x), however, at the cost of performance reduction (5x). Following common strategies in compression acceleration, we design to the best of our knowledge, the first hardware accelerator for the MPEG-G genomic data compression pipeline utilizing in-SRAM (Static Random-Access Memory) computing, referred to as iSCoder. We identify and analyze MatchC (Match Coding) and LutC (Lut Coding) as two bottleneck algorithms within this pipeline, propose two optimized in-SRAM algorithms, and design a unified hardware architecture for these algorithms, considering the characteristics of genomic data. Compared with 72-core Intel processors operating at 3.0 GHz, experimental results demonstrate that iSCoder achieves an average speedup of 131x for MatchC and 191x for LutC.
关键词	genomic sequencing data compression in-SRAM computing hardware accelerator
DOI	10.1007/s11390-025-5022-y
收录类别	SCI
语种	英语
WOS研究方向	Computer Science
WOS类目	Computer Science, Hardware & Architecture ; Computer Science, Software Engineering
WOS记录号	WOS:001666429600001
出版者	SPRINGER SINGAPORE PTE LTD
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/42884
专题	中国科学院计算技术研究所
通讯作者	Tan, Guang-Min
作者单位	1.Inst Comp Technol, Chinese Acad Sci, State Key Lab Processors, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100049, Peoples R China 3.Hong Kong Univ Sci & Technol, Hong Kong 999077, Peoples R China
推荐引用方式 GB/T 7714	Liu, Wan-Qi,Li, Ye-Wen,Tan, Guang-Min. iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2026:18.
APA	Liu, Wan-Qi,Li, Ye-Wen,&Tan, Guang-Min.(2026).iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,18.
MLA	Liu, Wan-Qi,et al."iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY (2026):18.