2022
DOI: 10.1038/s41592-022-01539-7
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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: 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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Cited by 284 publications
(291 citation statements)
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“…In particular, even higher-quality metagenomic assemblies are possible if HiFi reads from the Pacific Biosciences Sequel IIe system are available 46 . Also, the recent announcement of higher-quality reads from ONT could help improve assembly further and reduce costs 47 . Even as the sequencing landscape is constantly changing, the results from our study suggest that highquality population-specific metagenomic references are already feasible with a modest-sized cohort and limited sequencing resources.…”
Section: Discussionmentioning
confidence: 99%
“…In particular, even higher-quality metagenomic assemblies are possible if HiFi reads from the Pacific Biosciences Sequel IIe system are available 46 . Also, the recent announcement of higher-quality reads from ONT could help improve assembly further and reduce costs 47 . Even as the sequencing landscape is constantly changing, the results from our study suggest that highquality population-specific metagenomic references are already feasible with a modest-sized cohort and limited sequencing resources.…”
Section: Discussionmentioning
confidence: 99%
“…Higher basecall accuracy. Nanopore single-strand ('simplex') DNA basecall accuracy is 99% 11 . We believe that raising nanopore DRS accuracy to that level would revolutionize the field.…”
Section: Further Technical Improvements To Broaden Nanopore Drs Usementioning
confidence: 99%
“…Both E. coli and human genomes are sequenced using Oxford Nanopore Technologies (ONT) with R9-based chemistry [47]. This chemistry provides sequencing data with around 80-85% sequencing ac- 2 The E. coli dataset is available at: http://lab.loman.net/2016/07/30/ nanopore-r9-data-release/ curacy [142], which is slightly lower than the most recent chemistry (R10.4) that provides around 95-99% accuracy [143]. We include these less accurate datasets in our experiments to show the robustness and effectiveness of GenPIP in the presence of considerable sequencing inaccuracy.…”
Section: Evaluation Methodologymentioning
confidence: 99%