Nanopore sequencing technology, bioinformatics and applications

Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long rea...

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Bibliographic Details
Published in:	Nature biotechnology Vol. 39; no. 11; pp. 1348 - 1365
Main Authors:	Wang, Yunhao, Zhao, Yue, Bollas, Audrey, Wang, Yuru, Au, Kin Fai
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01.11.2021 Nature Publishing Group
Subjects:	631/114/2785 631/1647/48 631/61/514 Agriculture Bioinformatics Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedicine Biotechnology Computational Biology DNA sequencing Genomes Genomics High-Throughput Nucleotide Sequencing - methods Life Sciences Methods Nanopore Sequencing Nanopores Nucleotide sequencing Review Article Sequence Analysis, DNA - methods Technology Transcription Transcriptomes United States
ISSN:	1087-0156, 1546-1696, 1546-1696
Online Access:	Get full text
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Abstract	Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications. Au and colleagues outline the field of nanopore sequencing.
AbstractList	Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications. Au and colleagues outline the field of nanopore sequencing. Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications. Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.Au and colleagues outline the field of nanopore sequencing. Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
Audience	Academic
Author	Zhao, Yue Bollas, Audrey Au, Kin Fai Wang, Yunhao Wang, Yuru
AuthorAffiliation	2 Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA 3 These authors contributed equally: Yunhao Wang, Yue Zhao, Audrey Bollas 1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
AuthorAffiliation_xml	– name: 2 Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA – name: 1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA – name: 3 These authors contributed equally: Yunhao Wang, Yue Zhao, Audrey Bollas
Author_xml	– sequence: 1 givenname: Yunhao surname: Wang fullname: Wang, Yunhao organization: Department of Biomedical Informatics, The Ohio State University – sequence: 2 givenname: Yue surname: Zhao fullname: Zhao, Yue organization: Department of Biomedical Informatics, The Ohio State University, Biomedical Informatics Shared Resources, The Ohio State University – sequence: 3 givenname: Audrey surname: Bollas fullname: Bollas, Audrey organization: Department of Biomedical Informatics, The Ohio State University – sequence: 4 givenname: Yuru surname: Wang fullname: Wang, Yuru organization: Department of Biomedical Informatics, The Ohio State University – sequence: 5 givenname: Kin Fai orcidid: 0000-0002-9222-4241 surname: Au fullname: Au, Kin Fai email: kinfai.au@osumc.edu organization: Department of Biomedical Informatics, The Ohio State University, Biomedical Informatics Shared Resources, The Ohio State University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/34750572$$D View this record in MEDLINE/PubMed
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Review-3 content type line 23 K.F.A. designed the outline of the article. Yunhao Wang and A.B. collected information and prepared the materials for the ‘Technology development’ and ‘Data analysis’ sections. Y.Z. collected information and prepared the materials for the ‘Applications of nanopore sequencing’ section. K.F.A., Yunhao Wang, Y.Z. and A.B. wrote and revised the main text. Yuru Wang collected the references for the ‘Applications of nanopore sequencing’ section and prepared Fig. 1. Author contributions
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Snippet	Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and...
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SubjectTerms	631/114/2785 631/1647/48 631/61/514 Agriculture Bioinformatics Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedicine Biotechnology Computational Biology DNA sequencing Genomes Genomics High-Throughput Nucleotide Sequencing - methods Life Sciences Methods Nanopore Sequencing Nanopores Nucleotide sequencing Review Article Sequence Analysis, DNA - methods Technology Transcription Transcriptomes
Title	Nanopore sequencing technology, bioinformatics and applications
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