ArticlePloS one2021
Sequencing DNA with nanopores: Troubles and biases.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 326 papers, 2 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
326 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Pooled it
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials.Scientific reports · 2025Trial
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
- Experimental evolution of phage K enhances antibacterial activity against USA300 MRSA in lung infection models.Emerging microbes & infections · 2026Article
- Pedigree-Based comparison of short-read and long-read sequencing for forensic mitochondrial genome analysis.International journal of legal medicine · 2026Article
- Detecting pathogenic structural variation in families with undiagnosed rare disease in a national genome project.European journal of human genetics : EJHG · 2026Article
- K-MARVEL: K-Mer-based antimicrobial resistance virtual exploration lab.Nature communications · 2026Article
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Polus: a context-aware enhancement framework for DNA storage via transformer-based soft-decision decoding.Bioinformatics (Oxford, England) · 2026Article
- Simple birth-death-mutation models predict some-but not all-aspects of the experimental evolution of antibiotic resistance.PLoS computational biology · 2026Article
- Pathogenic mobile element insertion in theJournal of medical genetics · 2026Article
- Novel polymyxin resistance gene family mcr-12 from environmental Pigmentiphaga litoralis.Nature communications · 2026Article
- Article
- Pentanucleotide repeat instability and transmission in benign adult familial myoclonic epilepsy types 1, 4, and 8.Epilepsia · 2026Article
- Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.Viruses · 2026Article
266 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although over-estimated, offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.