Sequencing DNA with nanopores: Troubles and biases.

Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a t...

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Autores principales:	Clara Delahaye, Jacques Nicolas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/695188af719549a18bb2801b55bb6738
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spelling	oai:doaj.org-article:695188af719549a18bb2801b55bb67382021-12-02T20:13:51ZSequencing DNA with nanopores: Troubles and biases.1932-620310.1371/journal.pone.0257521https://doaj.org/article/695188af719549a18bb2801b55bb67382021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0257521https://doaj.org/toc/1932-6203Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although over-estimated, offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.Clara DelahayeJacques NicolasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0257521 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Clara Delahaye Jacques Nicolas Sequencing DNA with nanopores: Troubles and biases.
description	Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although over-estimated, offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.
format	article
author	Clara Delahaye Jacques Nicolas
author_facet	Clara Delahaye Jacques Nicolas
author_sort	Clara Delahaye
title	Sequencing DNA with nanopores: Troubles and biases.
title_short	Sequencing DNA with nanopores: Troubles and biases.
title_full	Sequencing DNA with nanopores: Troubles and biases.
title_fullStr	Sequencing DNA with nanopores: Troubles and biases.
title_full_unstemmed	Sequencing DNA with nanopores: Troubles and biases.
title_sort	sequencing dna with nanopores: troubles and biases.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/695188af719549a18bb2801b55bb6738
work_keys_str_mv	AT claradelahaye sequencingdnawithnanoporestroublesandbiases AT jacquesnicolas sequencingdnawithnanoporestroublesandbiases
_version_	1718374708850720768

Sequencing DNA with nanopores: Troubles and biases.

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