Abstract—There is no denying that Bioinformatics is one of
the most important realms for our forthcoming development. As
a demonstration of this fact, a plethora of new algorithms that
were published over the last decade. Those significantly boost up
the processes of biological analysis, especially for DNA
alignment. Despite their undeniable contributions, it is still far
more to state that DNA alignment has already achieved the ideal
performance. In this work, we focus on the DNA alignment
system which is based on our improved BWA-MEM algorithm
that we have already published. Besides that, we also propose
some optimization methods which was applied in order to
improve the performance as well as the stability of our entire
system. The system offers a speed-up by 46.52x when compared
with the other computing platforms.
Index Terms—DNA alignment, BWA-MEM algorithm,
FPGA, IP Core Seed extension.
Binh Kieu-Do-Nguyen and Cuong Pham-Quoc are with the Ho Chi Minh
City University of Technology – VNU-HCM, Ho Chi Minh City, Viet Nam
(corresponding author: Cuong Pham-Quoc; e-mail:
1770283@hcmut.edu.vn, cuongpham@hcmut.edu.vn).
Cong-Kha Pham is with the Department of Computer and Network
Engineering, Cluster II (Emerging Multi-interdisciplinary Engineering), The
University of Electro-Communications, the city of Chofu, Tokyo, Japan
(e-mail: phamck@uec.ac.jp).
Cite: Binh Kieu-Do-Nguyen, Cuong Pham-Quoc, and Cong-Kha Pham, "High-Performance FPGA-Based BWA-MEM Accelerator," International Journal of Machine Learning and Computing vol. 11, no. 3, pp. 256-261, 2021.
Copyright © 2021 by the authors. This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).