Fig. 1

Methylation calling from nanopore data and comparison to gold standard platforms. a UpSet plot of the intersections of CpG sites detected using DeepSignal, Nanopolish, Megalodon, and whole-genome bisulfite sequencing (WGBS) for NA12878. Because Encode WGBS workflow used index generated from GRCh38 assembly with alternative contiguous removed, only CpG methylations on main chromosomes (1–22 and X) were considered. b, c Pearson correlation matrix of methylation levels from the tools with WGBS (b) and Illumina’s 27k methylation array (c). For comparison to WGBS, only CpGs with at least 5 calls were considered. The number represents common CpGs in all methods. d Distribution of methylation over CpG islands (CGIs). e Distribution of methylation at transcription start (TSS) and end sites (TES). f Scatter plot of methylation level obtained from Nanopolish and Illumina’s 27k methylation array for NA19240 sample. Pearson correlation coefficient presented as r. g–h Distribution of methylation over common CpGs between Nanopolish and 27k array at CpG islands (CGIs) (g) or transcription start (TSS) and end sites (TES) (h). Gold standard methods for CpG methylation detection are indicated by an asterisk