Fig. 3

NanoMethPhase workflow and read phasing. a, b Haplotype block sizes following phasing of NA19240 and Colo829BL detected high-quality SNVs using WhatsHap. c NanoMethPhase workflow representing inputs, processing steps, and outputs. The output options can be requested independently to fit the needs. d–f Number of reads that were phased, filtered out, or could not be assigned to any phased SNV (left panel) and their length distribution (right panel, for ease in visualization reads with length < 50 kb are shown). d Obtained from NA19240 run 1 using nanopore phasing alone, e NA19240 run 1 trio phasing, and f Colo829BL sample. *NanoMethPhase phasing step ignores duplicated, QC failed, unmapped, and secondary reads. Supplementary reads also excluded by default but can be included as an optional parameter. The plots represent reads using default parameters