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GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller.

Shanshan Ren1, Nauman Ahmed1, Koen Bertels1

  • 1Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands.

BMC Genomics
|April 11, 2019
PubMed
Summary
This summary is machine-generated.

We developed a new GPU algorithm for efficient semi-global pairwise sequence alignment with traceback, significantly speeding up tools like GATK HaplotypeCaller (HC). This accelerates biological sequence analysis on modern hardware.

Keywords:
GATK HaplotypeCaller (HC)GPUsOptimal alignmentSemi-global alignment with traceback

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • High-Performance Computing

Background:

  • Pairwise sequence alignment is crucial for biological analysis tools.
  • Current GPU acceleration often omits optimal alignment traceback.
  • GATK HaplotypeCaller's semi-global alignment with traceback is challenging to accelerate on GPUs.

Purpose of the Study:

  • To develop an efficient GPU algorithm for semi-global pairwise sequence alignment with traceback.
  • To accelerate the GATK HaplotypeCaller (HC) software.
  • To enable faster and more efficient biological sequence analysis.

Main Methods:

  • Analyzed characteristics of semi-global alignment with traceback in GATK HC.
  • Proposed a novel GPU algorithm utilizing intra-task parallelization.
  • Implemented a backtracking matrix retrieval method incorporating match/mismatch lengths.

Main Results:

  • The GPU alignment kernel with traceback achieved up to 80x speedup on synthetic data and 14.14x on real data compared to CPU.
  • Integration into GATK HC resulted in a 2.3x overall speedup.
  • Achieved 1.34x speedup over GATK HC with GPU-accelerated pair-HMMs forward algorithm.

Conclusions:

  • The proposed GPU algorithm efficiently retrieves optimal alignments.
  • The method significantly accelerates GATK HC performance.
  • The approach is applicable to other pairwise alignment tasks and applications.