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

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 del...

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Autores principales: Sereika, Mantas, Kirkegaard, Rasmus Hansen, Karst, Søren Michael, Michaelsen, Thomas Yssing, Sørensen, Emil Aarre, Wollenberg, Rasmus Dam, Albertsen, Mads
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2022
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9262707/
https://www.ncbi.nlm.nih.gov/pubmed/35789207
http://dx.doi.org/10.1038/s41592-022-01539-7
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author Sereika, Mantas
Kirkegaard, Rasmus Hansen
Karst, Søren Michael
Michaelsen, Thomas Yssing
Sørensen, Emil Aarre
Wollenberg, Rasmus Dam
Albertsen, Mads
author_facet Sereika, Mantas
Kirkegaard, Rasmus Hansen
Karst, Søren Michael
Michaelsen, Thomas Yssing
Sørensen, Emil Aarre
Wollenberg, Rasmus Dam
Albertsen, Mads
author_sort Sereika, Mantas
collection PubMed
description 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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spelling pubmed-92627072022-07-09 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 Michaelsen, Thomas Yssing Sørensen, Emil Aarre Wollenberg, Rasmus Dam Albertsen, Mads Nat Methods Brief Communication 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. Nature Publishing Group US 2022-07-04 2022 /pmc/articles/PMC9262707/ /pubmed/35789207 http://dx.doi.org/10.1038/s41592-022-01539-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Communication
Sereika, Mantas
Kirkegaard, Rasmus Hansen
Karst, Søren Michael
Michaelsen, Thomas Yssing
Sørensen, Emil Aarre
Wollenberg, Rasmus Dam
Albertsen, Mads
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
title 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort 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
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9262707/
https://www.ncbi.nlm.nih.gov/pubmed/35789207
http://dx.doi.org/10.1038/s41592-022-01539-7
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