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^*

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Communication

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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.

Original language	English
Journal	Nature Methods
Volume	19
Issue number	7
Pages (from-to)	823-826
Number of pages	4
ISSN	1548-7091
DOIs	https://doi.org/10.1038/s41592-022-01539-7
Publication status	Published - 4 Jul 2022

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

Open Access articleFinal published version, 2.52 MBLicence: CC BY 4.0

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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, vol. 19, no. 7, pp. 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.
In: Nature Methods, Vol. 19, No. 7, 04.07.2022, p. 823-826.

Research output: Contribution to journal › Journal article › Communication

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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

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AU - Sørensen, Emil Aarre

AU - Wollenberg, Rasmus Dam

AU - Albertsen, Mads

PY - 2022/7/4

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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.

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JF - Nature Methods

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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

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Microflora Danica: The Microbiome of Denmark

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

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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

Bibliographical note

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Microflora Danica: The Microbiome of Denmark

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

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