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

Conference Paper (2018)
Author(s)

S. Ren (TU Delft - Computer Engineering)

N. Ahmed (TU Delft - Computer Engineering)

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

Zaid Al-Ars (TU Delft - Computer Engineering)

Research Group
Computer Engineering
Copyright
© 2018 S. Ren, N. Ahmed, K.L.M. Bertels, Z. Al-Ars
DOI related publication
https://doi.org/10.1109/BIBE.2018.00020
More Info
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Publication Year
2018
Language
English
Copyright
© 2018 S. Ren, N. Ahmed, K.L.M. Bertels, Z. Al-Ars
Research Group
Computer Engineering
Pages (from-to)
67-72
ISBN (electronic)
978-153866216-8
Reuse Rights

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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.

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