![]() ![]() ![]() Lastly, we provide an online DNA methylation database ( ) to display the DNA methylation levels detected by nanopore sequencing and bisulfite sequencing data across different genomic contexts. Furthermore, we demonstrate that 5hmC levels at least partly contribute to the discrepancy between bisulfite and nanopore sequencing. We show that the methylation prediction at regions with discordant DNA methylation patterns, intergenic regions, low CG density regions, and repetitive regions show room for improvement across all tools. The seven tools exhibit different performances across the evaluation criteria. We evaluate the per-read and per-site performance of CpG methylation prediction across different genomic contexts, CpG site coverage, and computational resources consumed by each tool. We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. ![]() Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection.
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