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 new 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.

中文翻译：

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用于纳米孔测序的CpG甲基化检测工具的系统基准测试

DNA甲基化在基因表达和基因组完整性的控制中起着基本作用。尽管有多种工具可以通过Nanopore测序对其进行检测，但其准确性仍然未知。在这里，我们介绍了使用单个读数，甲基化和非甲基化读数的对照混合物以及亚硫酸氢盐测序从纳米孔测序中检测CpG甲基化的工具的系统基准。我们发现工具在假阳性和假阴性之间进行权衡，并且相对于预期的甲基化频率值存在较高的离散度。我们描述了各种提高这些工具准确性的策略，包括一种新的共识方法METEORE（https://github.com/comprna/METEORE），基于来自两个或多个工具的预测的组合，显示出比单个工具更高的准确性。还提供了Snakemake管道以提高可重复性，并使我们的分析能够系统地应用于其他数据集。