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 )
