Improved GPU Implementations of the Pair-HMM Forward Algorithm for DNA Sequence Alignment

Enliang Li, Subho S. Banerjee, Sitao Huang, Ravishankar K. Iyer, Deming Chen

Research output: Chapter in Book/Report/Conference proceedingConference contribution


With the rise of Next-Generation Sequencing (NGS) technology, clinical sequencing services become more accessible but are also facing new challenges. The surging demand motivates developments of more efficient algorithms for computational genomics and their hardware acceleration. In this work, we use GPU to accelerate the DNA variant calling and its related alignment problem. The Pair-Hidden Markov Model (Pair-HMM) is one of the most popular and compute-intensive models used in variant calling. As a critical part of the Pair-HMM, the forward algorithm is not only a computational but data-intensive algorithm. Multiple previous works have been done in efforts to accelerate the computation of the forward algorithm by the massive parallelization of the workload. In this paper, we bring advanced GPU implementations with various optimizations, such as efficient host-device communication, task parallelization, pipelining, and memory management, to tackle this challenging task. Our design has shown a speedup of 783X comparing to the Java baseline on Intel single-core CPU, 31.88X to the C++ baseline on IBM Power8 multicore CPU, and 1.53X - 2.21X to the previous state-of-the-art GPU implementations over various genomics datasets.

Original languageEnglish (US)
Title of host publicationProceedings - 2021 IEEE 39th International Conference on Computer Design, ICCD 2021
PublisherInstitute of Electrical and Electronics Engineers Inc.
Number of pages8
ISBN (Electronic)9781665432191
StatePublished - 2021
Event39th IEEE International Conference on Computer Design, ICCD 2021 - Virtual, Online, United States
Duration: Oct 24 2021Oct 27 2021

Publication series

NameProceedings - IEEE International Conference on Computer Design: VLSI in Computers and Processors
ISSN (Print)1063-6404


Conference39th IEEE International Conference on Computer Design, ICCD 2021
Country/TerritoryUnited States
CityVirtual, Online


  • CUDA implementation
  • Computational Genomics
  • Forward algorithm
  • GPU acceleration
  • Pair-HMM

ASJC Scopus subject areas

  • Hardware and Architecture
  • Electrical and Electronic Engineering


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