PubReading [122] - Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing - Z. Yuen, E. Eyras et al

<p><strong>DNA methylation</strong> plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from <strong>Nanopore sequencing</strong>, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of <strong>CpG</strong> 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 (<a href="https://github.com/comprna/METEORE),">https://github.com/comprna/METEORE),</a> 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 <strong>systematic application</strong> of our analyses to other datasets. - doi.org/10.1038/s41467-021-23778-6 - 2021</p>