We developed a novel FSHD detection method based on ONT whole-genome sequencing for the comprehensive genetic analysis of FSHD that can distinguish the 4q35 and 10q26 D4Z4 repeat regions, determine the 4qA and 4qB haplotypes, identify pathogenetic contraction in D4Z4 RUs, detect the methylation status of the DUX4 region, and call FSHD2-related gene mutations simultaneously. This evidence concerns the gene SMCHD1 and facioscapulohumeral muscular dystrophy.