REPUTE: An OpenCL based Read Mapping Tool for Embedded Genomics
Sidharth Maheshwari1,a, Rishad Shafik1,b, Ian Wilson2, Alex Yakovlev1 and Amit Acharyya3
1School of Engineering, Newcastle University, Newcastle upon Tyne, UK
aS.Maheshwari2@ncl.ac.uk
bRishad.Shafik@newcastle.ac.uk
2Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
3Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India.
ABSTRACT
Genomics is transforming medicine from reactive to personalized, predictive, preventive and participatory (P4). The massive amount of data produced by genomics is a major challenge as it requires extensive computational capabilities, consuming large amounts of energy. A crucial prerequisite for computational genomics is genome assembly but the existing mapping tools used are predominantly software based, optimized for homogeneous high-performance systems. In this paper, we propose an OpenCL based REad maPper for heterogeneoUs sysTEms (REPUTE), which can use diverse and parallel compute and storage devices effectively. Core to this tool are dynamic programming based filtration and verification kernel to map the reads on multiple devices, concurrently. We show hardware/ software co-design and implementations of REPUTE across different platforms, and compare it with state-of-the-art mappers. We demonstrate the performance of mappers on two systems: 1) Intel CPU + 2×Nvidia GPUs; 2) HiKey970 embedded SoC with ARM Cortex-A73/A53 cores. The results show that REPUTE outperforms other read mappers in most cases producing up to 13× speedup with better or comparable accuracy. We also demonstrate that the embedded implementation can achieve up to 27× energy savings, enabling low-cost genomics.
Keywords: Genomics, Read Mapping, Embedded Acceleration, Heterogeneous Computing, OpenCL.
