SpecHap

SpecHap performs haplotype phasing using spectral graph theory to assemble haplotypes from sequencing data generated by whole-genome sequencing (WGS), Hi-C, 10X linked-reads, PacBio Single Molecule Real-Time (SMRT), and Oxford Nanopore long reads.

Key Features:

• Versatility across sequencing technologies: Supports WGS, Hi-C, 10X linked-reads, PacBio SMRT, and Oxford Nanopore long reads.
• Efficiency: Requires substantially less memory and CPU time than existing methods and, for example, phased the Ambystoma mexicanum genome in 6 CPU hours with 945MB peak memory.
• Scalability: Effectively handles both in silico and whole-genome sequencing datasets without memory overflow or excessive runtime.

Scientific Applications:

• Phasing diploid genomes: Reconstructs haplotypes from sequencing reads for diploid eukaryotic organisms.
• Studies of large and complex genomes: Applicable to genetic research involving species with large genomes, exemplified by Ambystoma mexicanum.

Methodology:

SpecHap applies spectral graph analysis (spectral graph theory) to process sequencing data and phase haplotypes.