Fig. 1

Overview of differential methylation analysis on ONT data using MetH5 and pycoMeth. Here, three biological samples are ONT-sequenced, base- and methylation-called, and haplotyped. The methylation caller output is stored in MetH5 format. Sample name and haplotype assignment for each read are stored as read groups in the MetH5 file (Fig. 2). PycoMeth methylome segmentation is performed, producing a consensus segmentation over all read-groups. Each segment is then tested for differential methylation or allele-specific methylation (in this example between-sample differences, ignoring haplotypes). Finally, pycoMeth generates a summary HTML report as well as detailed reports for all DMRs (Fig. 3)