ArticleCommunications biology2023
Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- K-MARVEL: K-Mer-based antimicrobial resistance virtual exploration lab.Nature communications · 2026Article
- Evaluation of Oxford nanopore sequencing for antimicrobial resistance surveillance inMicrobiology spectrum · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Targeted Next-Generation Sequencing in Drug-Resistant Tuberculosis: WHO Guidance and Practical Implementation Priorities.Biomedicines · 2026Review
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.mSystems · 2025Article
- Analysis of clinically relevant large tandem repeats using nanopore sequencing.Scientific reports · 2025Article
- A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology.bioRxiv : the preprint server for biology · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- A Comprehensive DNA Barcode Reference Library for the Macroinvertebrates of Scottish Seagrass Beds Using Oxford Nanopore Flongle Flowcells.Ecology and evolution · 2025Article
- Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA.NAR genomics and bioinformatics · 2025Article
- Article
- An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.Journal of clinical microbiology · 2025Article
- Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data.Journal of clinical microbiology · 2025Article
- Eliminating the Interference of Neighboring Nucleobases in Aerolysin for Nanopore Sequencing.ACS sensors · 2025Article
- Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.International journal of molecular sciences · 2025Article
- Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens likeJournal of clinical microbiology · 2025Article
- Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.Genome research · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modification types untrained in the basecalling models can seriously reduce the quality. Here we reports a set of ONT-sequenced genomes with unexpected low quality due to novel modification types. Demodification by whole-genome amplification significantly improved the quality but lost the epigenome. We also developed a reference-based method, Modpolish, for correcting modification-mediated errors while retaining the epigenome when a sufficient number of closely-related genomes is publicly available (default: top 20 genomes with at least 95% identity). Modpolish not only significantly improved the quality of in-house sequenced genomes but also public datasets sequenced by R9.4 and R10.4 (simplex). Our results suggested that novel modifications are prone to ONT systematic errors. Nevertheless, these errors are correctable by nucleotide demodification or Modpolish without prior knowledge of modifications.
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