Alternative name: HASH (Haplotype Assembly for Single Human) | HapCUT2
Allows haplotype assembly for diverse sequencing technologies. HapCUT is a maximum likelihood based algorithm that can assemble haplotypes for a diverse array of data modalities while other tools are specialized for certain subsets of data modalities. The software implements an iterative approach for modeling and estimating h-trans error probabilities de novo that reduces errors in assembled Hi-C haplotypes. It was assessed using data from fosmid-based dilution pool sequencing, 10X Genomics linked-read sequencing, single molecule real-time (SMRT) sequencing, and proximity ligation sequencing.