Fig. 6

The overlap of CpG sites predicted by methylation-calling tools. UpSet diagram shown at bottom of each panel (A and B) is for the CpG sites of the top thirty sets of intersections detected by each methylation-calling tool using (A) NA19240 and (B) NA12878 nanopore sequencing datasets. Venn diagram shown at the top of each panel (A and B) is for CpG sites detected by the four best-performing methylation-calling tools (Nanopolish, DeepSignal, Guppy, Megalodon), k is for thousand and M is for million. The numbers of CpGs in each intersection of Venn diagram can be found in Additional file 2: Table S11. Bar plot shown at the lower right of each panel (A and B) is for the total CpGs detected by each tool. For each methylation-calling tool, only the CpG sites covered by ≥ 3 reads were considered