GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads
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GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads Nauman Ahmed1,2* , Tong Dong Qiu1 , Koen Bertels1 and Zaid Al-Ars1 From The 18th Asia Pacific Bioinformatics Conference Seoul, Korea. 18-20 August 2020 *Correspondence: [email protected] 1 Delft University of Technology, Delft, Netherlands 2 University of Engineering and Technology Lahore, Lahore, Pakistan
Abstract Background: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo assembly of state-of-the-art third generation long DNA reads. Darwin is designed to be hardware-friendly and can be accelerated on specialized computer system hardware to achieve higher performance. Results: This work accelerates Darwin on GPUs. Using real Pacbio data, our GPU implementation on Tesla K40 has shown a speedup of 109x vs 8 CPU threads of an Intel Xeon machine and 24x vs 64 threads of IBM Power8 machine. The GPU implementation supports both linear and affine gap, scoring model. The results show that the GPU implementation can achieve the same high speedup for different scoring schemes. Conclusions: The GPU implementation proposed in this work shows significant improvement in performance compared to the CPU version, thereby making it accessible for utilization as a practical read overlapper in a DNA assembly pipeline. Furthermore, our GPU acceleration can also be used for performing fast SmithWaterman alignment between long DNA reads. GPU hardware has become commonly available in the field today, making the proposed acceleration accessible to a larger public. The implementation is available at https://github.com/Tongdongq/darwin-gpu. Keywords: Genomics, Read overlapper, De novo assembly, Long DNA reads, GPU acceleration
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