An Efficient GPU-based de Bruijn Graph Construction Algorithm for Micro-Assembly
Shanshan Ren (TU Delft - Electrical Engineering, Mathematics and Computer Science)
Nauman Ahmed (TU Delft - Electrical Engineering, Mathematics and Computer Science)
Koen Bertels (TU Delft - FTQC/Bertels Lab, TU Delft - (OLD)Quantum Computer Architectures)
Zaid Al-Ars (TU Delft - Electrical Engineering, Mathematics and Computer Science)
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Abstract
In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction algorithm for micro-assembly in the GATK HaplotypeCaller to improve its performance. Various synthetic datasets are used to compare the performance of the GPU-based de Bruijn graph construction implementation with the software-only baseline, which achieves a speedup of up to 3x. An experiment using two human genome datasets is used to evaluate the performance shows a speedup of up to 2.66x.