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App. Res. of Comp. Accepted Paper
Vol. 41, 2024 No. 12

Optimization of sequence alignment algorithm bwa

Hu Shuang1,2
Chen Changbo1,3
1. Chongqing Institute of Green & Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
2. School of Computer Science & Technology, Chongqing University of Posts & Telecommunications, Chongqing 400065, China
3. Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
DOI: 10.19734/j.issn.1001-3695.2024.05.0157

Abstract

Sequence alignment is a critical component of genomic data analysis, and improving its efficiency is vital for advancing sequencing technology applications in medicine, paleobiology, and other fields. This paper addresses the inefficiency in the SAMSE step of the BWA algorithm, caused by redundant index reads, by proposing a new algorithm called BWA*. Through process optimization, BWA* eliminates redundant reads of reference sequences and their indices in the SAMSE step. Additionally, the algorithm incorporates key parameter adjustments and multithreading optimizations to further enhance computational efficiency. Tests on real sequences from public databases show that the performance of BWA* in the SAMSE step is 7.11 to 8.61 times that of BWA, with an average of 7.84 times. Overall, BWA* achieves 1.25 to 1.70 times the performance of BWA, with an average of 1.47 times. In practical applications of ancient DNA sequence alignment, experiments demonstrate that the optimized BWA* surpasses the speed of BWA-MEM while maintaining the high accuracy characteristic of the original BWA.

Foundation Support

国家重点研发计划(2020YFA0712300)
重庆英才计划青年拔尖项目(2021000263)
重庆市院士牵头科技创新引导专项(cstc2021yszx-jcyjX0004,2022YSZX-JCX0011CSTB,CSTB2023YSZX-JCX0008)

Publish Information

DOI: 10.19734/j.issn.1001-3695.2024.05.0157
Publish at: Application Research of Computers Accepted Paper, Vol. 41, 2024 No. 12

Publish History

[2024-09-11] Accepted Paper

Cite This Article

胡爽, 陈长波. 序列比对算法BWA的优化 [J]. 计算机应用研究, 2024, 41 (12). (2024-09-11). https://doi.org/10.19734/j.issn.1001-3695.2024.05.0157. (Hu Shuang, Chen Changbo. Optimization of sequence alignment algorithm bwa [J]. Application Research of Computers, 2024, 41 (12). (2024-09-11). https://doi.org/10.19734/j.issn.1001-3695.2024.05.0157. )

About the Journal

  • Application Research of Computers Monthly Journal
  • Journal ID ISSN 1001-3695
    CN  51-1196/TP

Application Research of Computers, founded in 1984, is an academic journal of computing technology sponsored by Sichuan Institute of Computer Sciences under the Science and Technology Department of Sichuan Province.

Aiming at the urgently needed cutting-edge technology in this discipline, Application Research of Computers reflects the mainstream technology, hot technology and the latest development trend of computer application research at home and abroad in a timely manner. The main contents of the journal include high-level academic papers in this discipline, the latest scientific research results and major application results. The contents of the columns involve new theories of computer discipline, basic computer theory, algorithm theory research, algorithm design and analysis, blockchain technology, system software and software engineering technology, pattern recognition and artificial intelligence, architecture, advanced computing, parallel processing, database technology, computer network and communication technology, information security technology, computer image graphics and its latest hot application technology.

Application Research of Computers has many high-level readers and authors, and its readers are mainly senior and middle-level researchers and engineers engaged in the field of computer science, as well as teachers and students majoring in computer science and related majors in colleges and universities. Over the years, the total citation frequency and Web download rate of Application Research of Computers have been ranked among the top of similar academic journals in this discipline, and the academic papers published are highly popular among the readers for their novelty, academics, foresight, orientation and practicality.

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