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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'...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2017
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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has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly.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. |
format | Online Article Text |
id | pubmed-5770995 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
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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