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BIMSA: accelerating long sequence alignment using processing-in-memory

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اقرأ أكثر
  • معلومة اضافية
    • Publisher Information:
      2024-11-01
    • نبذة مختصرة :
      Motivation. Recent advances in sequencing technologies have stressed the critical role of sequence analysis algorithms and tools in genomics and healthcare research. In particular, sequence alignment is a fundamental building block in many sequence analysis pipelines and is frequently a performance bottleneck both in terms of execution time and memory usage. Classical sequence alignment algorithms are based on dynamic programming and often require quadratic time and memory with respect to the sequence length. As a result, classical sequence alignment algorithms fail to scale with increasing sequence lengths and quickly become memory-bound due to data-movement penalties. Results. Processing-In-Memory (PIM) is an emerging architectural paradigm that seeks to accelerate memory-bound algorithms by bringing computation closer to the data to mitigate data-movement penalties. This work presents BIMSA (Bidirectional In-Memory Sequence Alignment), a PIM design and implementation for the state-of-the-art sequence alignment algorithm BiWFA (Bidirectional Wavefront Alignment), incorporating new hardware-aware optimizations for a production-ready PIM architecture (UPMEM). BIMSA supports aligning sequences up to 100K bases, exceeding the limitations of state-of-the-art PIM implementations. First, BIMSA achieves speedups up to 22.24× (11.95× on average) compared to state-of-the-art PIM-enabled implementations of sequence alignment algorithms. Second, achieves speedups up to 5.84× (2.83× on average) compared to the highest-performance multicore CPU implementation of BiWFA. Third, BIMSA exhibits linear scalability with the number of compute units in memory, enabling further performance improvements with upcoming PIM architectures equipped with more compute units and achieving speedups up to 9.56× (4.7× on average).
      Postprint (published version)
    • الموضوع:
      Àrees temàtiques de la UPC::Enginyeria electrònica; Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica; Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat; Processing-In-memory; PIM; Bidirectional wavefront alignment; Bidirectional in-memory sequence alignment; Article
    • Availability:
      Open access content. Open access content
      Attribution 4.0 International
      http://creativecommons.org/licenses/by/4.0
      Open Access
    • Note:
      application/pdf
      English
    • Other Numbers:
      HGF oai:upcommons.upc.edu:2117/422267
      Alonso, A. [et al.]. BIMSA: accelerating long sequence alignment using processing-in-memory. "Bioinformatics", 1 Novembre 2024, vol. 40, núm. 11, btae631.
      1367-4803
      10.1093/bioinformatics/btae631
      1499889298
    • Contributing Source:
      UNIV POLITECNICA DE CATALUNYA
      From OAIster®, provided by the OCLC Cooperative.
    • الرقم المعرف:
      edsoai.on1499889298
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