Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Mantas Sereika; Rasmus Hansen Kirkegaard; Søren Michael Karst; Thomas Yssing Michaelsen; Emil Aarre Sørensen; Rasmus Dam Wollenberg; Mads Albertsen

doi:10.1038/s41592-022-01539-7

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Mantas Sereika, Rasmus Hansen Kirkegaard, Søren Michael Karst, Thomas Yssing Michaelsen, Emil Aarre Sørensen, Rasmus Dam Wollenberg, Mads Albertsen^*

^*Kontaktforfatter

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Formidling

171 Citationer (Scopus)

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Abstract

Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.

Originalsprog	Engelsk
Tidsskrift	Nature Methods
Vol/bind	19
Udgave nummer	7
Sider (fra-til)	823-826
Antal sider	4
ISSN	1548-7091
DOI	https://doi.org/10.1038/s41592-022-01539-7
Status	Udgivet - 4 jul. 2022

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10.1038/s41592-022-01539-7Licens: CC BY 4.0

Open Access articleForlagets udgivne version, 2,52 MBLicens: CC BY 4.0

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Microflora Danica: The Microbiome of Denmark
Albertsen, M. (PI (principal investigator)), Nielsen, P. H. (PI (principal investigator)), Jensen, T. B. N. (Projektdeltager), Sørensen, E. A. (Projektdeltager), Sereika, M. (Projektdeltager), Dottorini, G. (Projektdeltager), Petriglieri, F. (Projektdeltager), Jørgensen, V. R. (Projektdeltager), Kirkegaard, R. H. (Projektdeltager), Yang, Y. (Projektdeltager), Karst, S. M. (Projektdeltager), Giguere, A. T. (Projektdeltager), Knutsson, S. (Projektdeltager), Singleton, C. M. (Projektdeltager), Dueholm, M. K. D. (Projektdeltager), Mølvang Dall, S. (Projektdeltager), Kristensen, J. M. (Projektdeltager) & Delogu, F. (Projektdeltager)
Poul Due Jensens Fond
01/01/2019 → 31/12/2025
Projekter: Projekt › Forskning
Deciphering the role of microbial dark matter by novel DNA sequencing approaches
Albertsen, M. (PI (principal investigator)), Karst, S. M. (Projektdeltager), Kirkegaard, R. H. (Projektdeltager) & Yssing Michaelsen, T. (Projektdeltager)
Villum Fonden
01/01/2017 → 01/01/2022
Projekter: Projekt › Forskning

Citationsformater

Sereika, M., Kirkegaard, R. H., Karst, S. M., Yssing Michaelsen, T., Sørensen, E. A., Wollenberg, R. D., & Albertsen, M. (2022). Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nature Methods, 19(7), 823-826. https://doi.org/10.1038/s41592-022-01539-7

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abstract = "Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.",

author = "Mantas Sereika and Kirkegaard, {Rasmus Hansen} and Karst, {S{\o}ren Michael} and {Yssing Michaelsen}, Thomas and S{\o}rensen, {Emil Aarre} and Wollenberg, {Rasmus Dam} and Mads Albertsen",

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Sereika, M , Kirkegaard, RH, Karst, SM, Yssing Michaelsen, T, Sørensen, EA , Wollenberg, RD & Albertsen, M 2022, 'Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing', Nature Methods, bind 19, nr. 7, s. 823-826. https://doi.org/10.1038/s41592-022-01539-7

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. / Sereika, Mantas ; Kirkegaard, Rasmus Hansen; Karst, Søren Michael et al.
I: Nature Methods, Bind 19, Nr. 7, 04.07.2022, s. 823-826.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Formidling

TY - JOUR

T1 - Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

AU - Sereika, Mantas

AU - Kirkegaard, Rasmus Hansen

AU - Karst, Søren Michael

AU - Yssing Michaelsen, Thomas

AU - Sørensen, Emil Aarre

AU - Wollenberg, Rasmus Dam

AU - Albertsen, Mads

PY - 2022/7/4

Y1 - 2022/7/4

N2 - Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.

AB - Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.

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U2 - 10.1038/s41592-022-01539-7

DO - 10.1038/s41592-022-01539-7

M3 - Journal article

C2 - 35789207

SN - 1548-7091

VL - 19

SP - 823

EP - 826

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Abstract

Bibliografisk note

Adgang til dokumentet

AUB Link

Andre filer og links

Fingeraftryk

Projekter

Microflora Danica: The Microbiome of Denmark

Deciphering the role of microbial dark matter by novel DNA sequencing approaches

Citationsformater