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The long reads ahead: de novo genome assembly using the MinION

Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION'...

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Detalles Bibliográficos
Autores principales: de Lannoy, Carlos, de Ridder, Dick, Risse, Judith
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770995/
https://www.ncbi.nlm.nih.gov/pubmed/29375809
http://dx.doi.org/10.12688/f1000research.12012.2
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author de Lannoy, Carlos
de Ridder, Dick
Risse, Judith
author_facet de Lannoy, Carlos
de Ridder, Dick
Risse, Judith
author_sort de Lannoy, Carlos
collection PubMed
description Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly. As the MinION is approaching a state of maturity, its user community would benefit from a thorough comparative benchmarking effort of de novo assembly pipelines in the near future. An earlier version of this article can be found on  bioRxiv.
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spelling pubmed-57709952018-01-26 The long reads ahead: de novo genome assembly using the MinION de Lannoy, Carlos de Ridder, Dick Risse, Judith F1000Res Review Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly. As the MinION is approaching a state of maturity, its user community would benefit from a thorough comparative benchmarking effort of de novo assembly pipelines in the near future. An earlier version of this article can be found on  bioRxiv. F1000 Research Limited 2017-12-12 /pmc/articles/PMC5770995/ /pubmed/29375809 http://dx.doi.org/10.12688/f1000research.12012.2 Text en Copyright: © 2017 de Lannoy C et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
de Lannoy, Carlos
de Ridder, Dick
Risse, Judith
The long reads ahead: de novo genome assembly using the MinION
title The long reads ahead: de novo genome assembly using the MinION
title_full The long reads ahead: de novo genome assembly using the MinION
title_fullStr The long reads ahead: de novo genome assembly using the MinION
title_full_unstemmed The long reads ahead: de novo genome assembly using the MinION
title_short The long reads ahead: de novo genome assembly using the MinION
title_sort long reads ahead: de novo genome assembly using the minion
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770995/
https://www.ncbi.nlm.nih.gov/pubmed/29375809
http://dx.doi.org/10.12688/f1000research.12012.2
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