We use cookies to improve your experience with our site.

Indexed in:

SCIE, EI, Scopus, INSPEC, DBLP, CSCD, etc.

Submission System
(Author / Reviewer / Editor)
Advanced Search
Turn off MathJax
Article Contents
Abstract
Supplements
Ye-Wen Li, Guang-Ming Tan, Xue-Qi Li. FuHsi: Shifting Base-calling Closer to Sequencer via In-cache Acceleration[J]. Journal of Computer Science and Technology. DOI: 10.1007/s11390-025-3886-5
Citation: Ye-Wen Li, Guang-Ming Tan, Xue-Qi Li. FuHsi: Shifting Base-calling Closer to Sequencer via In-cache Acceleration[J]. Journal of Computer Science and Technology. DOI: 10.1007/s11390-025-3886-5
shu

FuHsi: Shifting Base-calling Closer to Sequencer via In-cache Acceleration

  • 1.

    State Key Laboratory of Processors, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China

  • 2.

    School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China

Funds: The work is supported in part by NKRDP (2021YFB0300202), the National Key R&D Program of China under Grants No. 2022YFB4500403, National Natural Science Foundation of China, under Grant No. 62202454, 62032023, T2125013.
More Information
  • Received Date: October 22, 2023
  • Revised Date: July 05, 2024
  • Accepted Date: January 13, 2025
    Abstract
  • Base-calling is an essential step in the analysis of third-generation genome data. Many previous hardware efforts aimed at enhancing processing in the workflow. However, an order of magnitude throughput gap still exists. In this paper, we propose FuHsi to improve the end-to-end throughput of the base-calling process. FuHsi is an in-cache accelerator that only introduces three components to the traditional CPUs in the sequencer. We propose FuHsi Cache, which offloads the bottleneck operations to cache arithmetic. Specifically, we accelerate beam search, string conversion, and MAC using algorithm/hardware co-design. We also introduce FuHsi APIs and FuHsi Controller to provide coarse-grained control for FuHsi Cache. Experimental results show that FuHsi can achieve 45.7×, 113.1×, and 100×throughput per watt speedup when compared with an NVIDIA Jetson baseline, an NVIDIA A100 GPU baseline, and the Helix accelerator, respectively. FuHsi can provide base-calling requests for up to 15 ONT sequencers simultaneously.
    • FullText(HTML)
    • References (0)
    • Relative Articles
  • Supplements (2)

  • Others

Catalog

    Get Citation
    PDF
    XML
    Article views (48) PDF downloads (7) Cited by()
    Related

    Copyright ©2025 JCST, All Rights Reserved     京ICP备05002829号-1

    Institute of Computing Technology, Chinese Academy of Sciences
    P.O. Box 2704, Beijing 100190, P.R. China

    Tel.: 86-10-62610746 E-mail: jcst@ict.ac.cn

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return