ArticleBMC bioinformatics2020
GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed, 7 citations in OpenAlex.
- WFA-GPU: gap-affine pairwise read-alignment using GPUs.Bioinformatics (Oxford, England) · 2023Article
- Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.Bioinformatics (Oxford, England) · 2023Article
- A framework for high-throughput sequence alignment using real processing-in-memory systems.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIn 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.
resultsThis 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.
conclusionsThe 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 Smith-Waterman 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 .
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