Hardware-assisted High-performance DNA Alignment System
Pages 45 - 50
Abstract
The investigations of DNA become more and more important in this era. A plethora of new algorithms that were published over the last decade are apparent evidences for this fact. In the DNA's researches, alignment is one of the most important steps that is especially taken care and continuously developed. Despite they already have a lot of algorithms for this problem, and some of them provide impressive enhancements. But it is still far more to state that DNA alignment has already achieved the ideal performance. Therefore, in this work, we promote an efficient architecture which is based on our improved BWA-MEM algorithm that we have already published in [14]. Beside that, we also propose a communication protocol as well as as its API in order to ensure the accuracy and stability of the system. The system offers a speed-up by 18.14x when compared with modern computing platforms.
References
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N. Ahmed, V. Sima, E. Houtgast, K. Bertels, and Z. Al-Ars. 2015. Heterogeneous hardware/software acceleration of the BWA-MEM DNA alignment algorithm. In 2015 IEEE/ACM International Conference on Computer-Aided Design (ICCAD). 240--246. https://doi.org/10.1109/ICCAD.2015.7372576
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Khaled Benkrid, Ali Akoglu, Cheng Ling, Yang Song, Ying Liu, and Xiang Tian. 2012. High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP. Int. J. Reconfig. Comp. 2012 (2012), 752910:1-752910:15.
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Hongzhi Cao, Yu Wang, Wei Zhang, Xianghua Chai, Xiandong Zhang, Shiping Chen, Fan Yang, Caifen Zhang, Yulai Guo, Ying Liu, Zhoubiao Tang, Caifen Chen, Yaxin Xue, Hefu Zhen, Yinyin Xu, Bin Rao, Tao Liu, Meiru Zhao, Wenwei Zhang, and Jian Li. 2014. A Short-Read Multiplex Sequencing Method for Reliable, Cost-Effective and High-Throughput Genotyping in Large-Scale Studies. Human mutation 34 (02 2014). https://doi.org/10.1002/humu.22439
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Y. Chen, J. Cong, J. Lei, and P. Wei. 2015. A Novel High-Throughput Acceleration Engine for Read Alignment. In 2015 IEEE 23rd Annual International Symposium on Field-Programmable Custom Computing Machines. 199--202. https://doi.org/10.1109/FCCM.2015.27
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E. J. Houtgast, V. Sima, K. Bertels, and Z. Al-Ars. 2015. An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm. In 2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS). 221--227. https://doi.org/10.1109/SAMOS.2015.7363679
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B Langmead. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. J. Genome Biol. 25 (01 2009), 423--433.
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Heng Li. 2010. Burrows-Wheeler Aligner. Retrieved July 29, 2019 from http://biobwa.sourceforge.net/
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Heng Li. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv 1303 (03 2013).
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Hezdri, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, and Jun Wang. 2009. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics (Oxford, England) 25 (07 2009), 1966-7. https://doi.org/10.1093/bioinformatics/btp336
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Cuong Pham-Quoc, Kieu Binh, and Tran Ngoc Thinh. 2018. An FPGA-Based Seed Extension IP Core for BWA-MEM DNA Alignment. 1--6. https://doi.org/10.1109/ACOMP.2018.00009
[12]
Cuong Pham-Quoc, Kieu Binh, and Tran Ngoc Thinh. 2019. A high-performance FPGA-based BWA-MEM DNA sequence alignment. Concurrency and Computation: Practice and Experience (05 2019). https://doi.org/10.1002/cpe.5328
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Temple F. Smith and Michael S. Waterman. 1981. Identification of common molecular subsequences. Journal of molecular biology 147 1 (1981), 195--7.
Index Terms
- Hardware-assisted High-performance DNA Alignment System
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Published In
February 2020
163 pages
ISBN:9781450376594
DOI:10.1145/3385209
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Published: 06 June 2020
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ICIIT 2020
ICIIT 2020: 2020 5th International Conference on Intelligent Information Technology
February 19 - 22, 2020
Hanoi, Viet Nam
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