Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

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...

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Bibliographic Details
Published in:Nature communications 2021-06, Vol.12 (1), p.3438-3438, Article 3438
Main Authors: Yuen, Zaka Wing-Sze, Srivastava, Akanksha, Daniel, Runa, McNevin, Dennis, Jack, Cameron, Eyras, Eduardo
Format: Article
Language:English
Subjects:
45/23
631/114/2785
631/114/794
631/1647/514/1948
631/208/177
Accuracy
Algorithms
Benchmarking
Benchmarks
Bisulfite
CpG islands
CpG Islands - genetics
CRISPR-Associated Protein 9 - metabolism
Cytosine - metabolism
Deoxyribonucleic acid
DNA
DNA - metabolism
DNA methylation
DNA Methylation - genetics
DNA sequencing
Escherichia coli - genetics
Gene expression
Genome, Bacterial
Genomes
Humanities and Social Sciences
multidisciplinary
Nanopore Sequencing
ROC Curve
Science
Science (multidisciplinary)
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Summary: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. Several existing algorithms predict the methylation of DNA using Nanopore sequencing signals, but it is unclear how they compare in performance. Here, the authors benchmark the performance of several such tools, and propose METEORE, a consensus tool that improves prediction accuracy.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-021-23778-6