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

Nat Methods. 2022 Jul;19(7):823-826. doi: 10.1038/s41592-022-01539-7. Epub 2022 Jul 4.

Authors

Mantas Sereika^#¹, Rasmus Hansen Kirkegaard^#^{1

2}, Søren Michael Karst¹, Thomas Yssing Michaelsen¹, Emil Aarre Sørensen¹, Rasmus Dam Wollenberg³, Mads Albertsen⁴

Affiliations

¹ Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
² Joint Microbiome Facility, University of Vienna, Vienna, Austria.
³ DNASense ApS, Aalborg, Denmark.
⁴ Center for Microbial Communities, Aalborg University, Aalborg, Denmark. [email protected].

^# Contributed equally.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Bacterial
High-Throughput Nucleotide Sequencing
Metagenome*
Nanopores*
Sequence Analysis, DNA