The Third Revolution in Sequencing Technology

The Third Revolution in Sequencing Technology  第三代测序技术

Erwin L van Dijk 1, Yan Jaszczyszyn 2, Delphine Naquin 2, Claude Thermes 2

Affiliations expand

• PMID: 29941292
•  
• DOI: 10.1016/j.tig.2018.05.008

Abstract

Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.

四十年前，桑格测序的出现是革命性的，因为它第一次使完整的基因组序列得以破译。
第二次革命随着新一代测序技术的出现而到来，新一代测序技术使得基因组测序更加便宜和快捷。
然而，NGS方法有几个缺点和缺陷，最明显的是它们的读取时间很短。
最近，第三代/长读方法出现了，它可以产生前所未有的高质量的基因组组合。
此外，这些技术可以直接检测到本地DNA的表观遗传修饰，并允许不需要组装的全转录本测序。
这标志着测序技术的第三次革命。
这里，我们回顾并比较各种长读方法。
我们讨论它们的应用和各自的优缺点，并提供未来的展望。

Keywords: long-read sequencing; nanopore sequencing; next-generation sequencing; single-molecule real-time sequencing; synthetic long-read sequencing; third-generation sequencing.

 

Highlights

Long-read/third-generation sequencing technologies are causing a new revolution in genomics as they provide a way to study genomes, transcriptomes, and metagenomes at an unprecedented resolution.

SMRT and nanopore sequencing allow for the first time the direct study of different types of DNA base modifications.

Moreover, nanopore technology can sequence directly RNA and identify RNA base modifications.

Owing to the portability of the MinION and the existence of extremely simple library preparation methods, nanopore technology allows the performance of high-throughput sequencing for the first time in the field and at remote places. This is of tremendous importance for the survey of outbreaks in developing countries.

Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.

长期阅读的/第三代测序技术正在引发基因组学的一场新的革命，因为它们提供了一种以前所未有的分辨率研究基因组、转录组和宏基因组的方法。

SMRT和纳米孔测序首次允许直接研究不同类型的DNA碱基修饰。

此外，纳米孔技术可以直接测序RNA，识别RNA碱基修饰。

由于MinION的便携性和极其简单的文库制备方法，纳米孔技术首次实现了现场和偏远地区的高通量测序。
这对于调查发展中国家的疫情极其重要。

四十年前，桑格测序的出现是革命性的，因为它第一次使完整的基因组序列得以破译。
第二次革命随着新一代测序技术的出现而到来，新一代测序技术使得基因组测序更加便宜和快捷。
然而，NGS方法有几个缺点和缺陷，最明显的是它们的读取时间很短。
最近，第三代/长读方法出现了，它可以产生前所未有的高质量的基因组组合。
此外，这些技术可以直接检测到本地DNA的表观遗传修饰，并允许不需要组装的全转录本测序。
这标志着测序技术的第三次革命。
这里，我们回顾并比较各种长读方法。
我们讨论它们的应用和各自的优缺点，并提供未来的展望。