ArticleNature communications2021
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05765864 (Influences on and Prevention of Self-harm Behaviour Among the Most At-risk Adolescents), which is not on this map. Cited by 107 papers.
What it found
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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.
Influences on and Prevention of Self-harm Behaviour Among the Most At-risk Adolescents
Who cites it
107 citing papers in PubMed, 170 citations in OpenAlex.
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- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- Population-scale detection of methylation outliers from long-read genome sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Genome-wide and gene-specific DNA methylation across developmental stages in Pogonomyrmex californicus: A socially polymorphic ant.Insect molecular biology · 2026Article
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- The Evolving Role of Genomic Technologies in Multiple Myeloma: Implications for Diagnosis, Risk Stratification and Resistance.Molecular diagnosis & therapy · 2026Review
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- SquiDBase: a community resource of raw nanopore data from microbes.NAR genomics and bioinformatics · 2026Article
- LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns.bioRxiv : the preprint server for biology · 2026Article
- SnakeBITE: A SNAKEmake-Based Interface for Third-Generation Sequencing Data Analysis.Biomolecules · 2026Article
- Functional and Epigenomic Consequences ofInternational journal of molecular sciences · 2026Article
- Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.Nucleic acids research · 2026Review
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- Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada's national platform for genome sequencing and analysis.Frontiers in genetics · 2026Article
- Epigenotoxicity: Decoding the epigenetic imprints of genotoxic agents and their implications for regulatory genetic toxicology.Environmental and molecular mutagenesis · 2025Review
- An allele-resolved nanopore-guided tour of the human placental methylome.Nature communications · 2025Article
47 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
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE ( https://github.com/comprna/METEORE ), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.
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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.