An Efficient GPU-based de Bruijn Graph Construction Algorithm for Micro-Assembly

Conference paper (2018)

Authors

S. Ren Computer Engineering -

N. Ahmed Computer Engineering -

K.L.M. Bertels (OLD)Quantum Computer Architectures , FTQC/Bertels Lab

Z. Al-Ars Computer Engineering -

Zaid Al-Ars Computer Engineering -

Research Group

Computer Engineering () (TU Delft)

DOI: https://doi.org/10.1109/BIBE.2018.00020

GPU acceleration De Bruijn graph construction Micro-assembly Repeat k-mers

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Published Date

2018

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Quantum & Computer Engineering

Research Group

Computer Engineering

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.

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