SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing

Segmental duplications are important for understanding human diseases and evolution. The challenge to distinguish allelic and duplication sequences has hindered their phased assembly as well as characterization of structural variant calls. Here we have developed a novel graph-based approach that leverages single nucleotide differences in overlapping reads to distinguish allelic and duplication sequences information from long read accurate PacBio HiFi sequencing. These differences enable to generate allelic and duplication-specific overlaps in the graph to spell out phased assembly used for structural variant calling. We have applied our method to three public genomes: CHM13, NA12878 and HG002. Our method resolved 86% of duplicated regions fully with contig N50 up to 79 kb and produced