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| Signal Processing for Nanopore Sequencing and Its Application in DNA Data Storage |
GE Qi1,ZHANG Peng1,HAN Ming-zhe2,3,YANG Jin-sheng1,ZHANG Da-lu4,*( ),CHEN Wei-gang1,3 |
1 School of Microelectronics, Tianjin University, Tianjin 300072, China
2 School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
3 Frontiers Science Center for Synthetic Biology (MOE), Tianjin University, Tianjin 300072, China
4 China National Center for Biotechnology Development, Beijing 100039, China |
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Abstract With the continuous update of high-throughput sequencing technologies, the third-generation sequencing technology that can read nucleotide sequences at the single-molecule level has developed rapidly. Nanopore sequencing technology is its representative single-molecule sequencing technology, which realizes base calling by detecting the characteristic changes of electrical current when the DNA single-stranded molecule is passing through a nanopore channel. Compared with the traditional first-generation and the next-generation sequencing (NGS) technologies, the nanopore sequencing of DNA has great advantages in device portability, base acquisition speed and read length, which has attracted much attention. With the continuous development of nanopore sequencing technologies, various signal processing schemes and biological information processing tools for nanopore sequencing have been developed, and base calling and model simulation are two of the key research directions. The fundamental principle and signal processing flow of nanopore sequencing are surveyed, the current challenges are discussed, then the development trend of base calling and nanopore model simulation in recent years are summarized, and the performance of different base calling methods are compared by using real sequencing reads. Then, an integrated simulation platform for the evaluation of signal processing algorithms of nanopore sequencing is developed. Furthermore, with the explosive growth of global data volume, DNA data storage is becoming a promising medium for future massive data storage, and the use of nanopore for sequencing and reading is a very effective method. The application progress of the nanopore sequencing technology for DNA data storage is summarized, and its feasibility is analyzed. The rapid readout method of artificial chromosome data storage based on nanopore sequencing is analyzed, and the application of the simulation of nanopore sequencing reads combined with actual sequencing data in DNA data storage is discussed, which provides a reference for the development of a suitable DNA data storage program.
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Received: 14 April 2021
Published: 31 August 2021
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Corresponding Authors:
Da-lu ZHANG
E-mail: zhangdl@cncbd.org.cn
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