SpecHap: a fast haplotyping method based on spectral graph theory

Haplotype phasing has fundamental implications in human genetics study. With rapid advancing of technology, novel sequencing protocols including linked-reads and third generation sequencing technology which enables whole genome haplotype phasing have been developed. Many phasing software, most of which bases on resources intensive heuristic algorithms, have been developed to handle various sequencing technologies. Here, we present a novel approach called SpecHap that adopts spectral graph theory for fast diploid haplotype construction from diverse sequencing protocols. On both simulated and real sequencing data set, SpecHap achieved higher sensitivity than existing tools, demonstrating high computational efficiency while preserving the length of the phased genomic regions.