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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2021, Vol. 41 Issue (8): 75-89    DOI: 10.13523/j.cb.2104018
综述     
纳米孔测序信号处理及其在DNA数据存储的应用
葛奇1,张鹏1,韩明哲2,3,杨晋生1,张大璐4,*(),陈为刚1,3
1 天津大学微电子学院 天津 300072
2 天津大学化工学院 天津 300072
3 教育部合成生物学前沿科学中心 天津大学 天津 300072
4 中国生物技术发展中心 北京 100039
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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摘要：

随着高通量测序技术的不断更新,可以在单个分子水平读取核苷酸序列的第三代测序技术迅速发展,纳米孔测序技术是其具有代表性的单分子测序技术,该技术通过检测DNA单链分子穿过纳米孔时引起的跨膜电流信号的变化,实现碱基识别。纳米孔测序仪在便携性、碱基读取速度、测序读段长度等方面较传统的第一代与第二代测序技术都有明显优势。随着纳米孔测序技术的不断发展成熟,与其配套的各种信号处理与生物信息处理工具也迅速涌现,碱基识别和模型仿真是其中两个较为关键的研究方向。首先介绍纳米孔测序基本原理与信号处理流程,探讨其目前面临的挑战,归纳近年来在碱基识别与纳米孔模型仿真两个方面的主要进展与发展趋势,并用实测数据比较了不同碱基识别方法的性能。继而搭建了纳米孔测序集成仿真平台,为信号处理算法的评估提供支撑。进一步,随着全球数据量的爆发式增长,DNA数据存储正成为未来非常有潜力的海量数据存储方式,采用纳米孔测序读出是一种非常有效的方法。总结了纳米孔测序技术在DNA数据存储中的应用进展,分析了其可行性。分析了基于纳米孔测序实现的人工染色体数据存储的快速读出方法,探讨了与实际测序数据结合的纳米孔测序读段仿真在DNA数据存储中的应用,为开发适合DNA数据存储的方案提供参考。
关键词： 纳米孔测序;  碱基识别;  纳米孔信号处理;  DNA数据存储    
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.
Key words: Nanopore sequencing    Base calling    Nanopore signal processing    DNA data storage
收稿日期: 2021-04-14 出版日期: 2021-08-31
ZTFLH:  Q819  
通讯作者: 张大璐     E-mail: zhangdl@cncbd.org.cn
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引用本文:

葛奇,张鹏,韩明哲,杨晋生,张大璐,陈为刚. 纳米孔测序信号处理及其在DNA数据存储的应用[J]. 中国生物工程杂志, 2021, 41(8): 75-89.

GE Qi,ZHANG Peng,HAN Ming-zhe,YANG Jin-sheng,ZHANG Da-lu,CHEN Wei-gang. Signal Processing for Nanopore Sequencing and Its Application in DNA Data Storage. China Biotechnology, 2021, 41(8): 75-89.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2104018    或    https://manu60.magtech.com.cn/biotech/CN/Y2021/V41/I8/75

图1  纳米孔测序的基本流程与基本原理
碱基识别软件 是否开源 程序语言 输入数据类型 核心计算模型 开发团队
Nanocall 是 C++ 分段事件 隐马尔科夫模型 David等[41]
Nanonet 是 C++ 分段事件 循环神经网络 ONT公司
DeepNano 是 Python 分段事件 循环神经网络 Boza等[42]
BasecRAWller 否 - 原始电流信号 循环神经网络 Stoiber等[43]
Chiron 是 Python 原始电流信号 循环神经网络 Teng等[44]
Albacore 否 Python 原始电流信号 循环神经网络 ONT公司
Guppy 否 - 原始电流信号 循环神经网络 ONT公司
Scrappie 是 C 分段事件或原始电流信号 循环神经网络 ONT公司
Flappie 是 C 原始电流信号 循环神经网络 ONT公司
表1  纳米孔测序的碱基识别软件比较
图2  碱基识别软件性能比较
图3  IDS有记忆错误模型
仿真软件 程序语言 是否生成仿真读段 是否生成仿真信号 是否模拟噪声特性 开发团队
ReadSim Python 是 否 否 Lee等[50]
SiLiCO Python 是 否 否 Baker等[51]
NanoSim Python 是 否 是 Yang等[52]
DeepSimulator Python 是 是 是 Li等[53,54]
NanosigSim Python 是 是 是 Chen等[55]
表2  纳米孔测序仿真软件比较
图4  纳米孔测序仿真平台
图5  数据存储专用人工染色体的数据读出验证平台[58]
图6  利用实际测序数据训练的基于三代纳米孔测序的DNA数据存储仿真流程
图7  基于纳米孔测序的仿真数据的寻址方式研究
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