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bioRxiv · 10.64898/2025.12.17.694868

Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment

Kallenborn, F.·Dabbaghie, F.·Steinegger, M.·Schmidt, B.
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Abstract

BackgroundThe continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic time complexity. This motivates the need for a library of efficient implementations on modern GPUs for a variety of alignment algorithms for different types of sequence data including DNA, RNA, and proteins. ResultsAccelign is a library of accelerated pairwise sequence alignment algorithms for CUDA-enabled GPUs. Its parallelization strategy is based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes supporting one-to-one, one-to-many or all-to-all pairwise sequence alignments. This leads to a peak performance between 16.1 TCUPS and 9.1 TCUPS for computing optimal global alignment scores with linear gaps and affine gap penalties on a single RTX PRO 6000 Blackwell GPU, respectively. In addition, our library demonstrates significant speedups in several real-world case studies over prior CPU-based (SeqAn, Parasail, BSalign) and GPU-based libraries (ADEPT, GASAL2), and can even outperform highly customized algorithms (WFA-GPU, CUDASW++4.0). Furthermore, the performance of our approach scales linearly with the number of employed GPUs, which makes it feasible to exploit multi-GPU nodes for increased processing speeds. ConclusionAccelign provides significant speedups for commonly used pairwise alignment algorithms compared to prior implementations. It is freely available at https://github.com/fkallen/Accelign.

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Kallenborn, F., Dabbaghie, F., Steinegger, M., Schmidt, B.. 2025-12-19. Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment. https://doi.org/10.64898/2025.12.17.694868

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