BOL

HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to:

NGS short reads (Illumina HiSeq)
clone-based sequencing (Fosmid or BAC clones)
SMRT reads (PacBio)
Oxford Nanopore reads
10X Genomics Linked-Reads
proximity-ligation (Hi-C) reads
high-coverage sequencing (>40x coverage-per-SNP) using above technologies
combinations of the above technologies (e.g. scaffold long reads with Hi-C reads)
See below for specific examples of command line options and best practices for some of these technologies.

NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants.

If you use HapCUT2 in your research, please cite:

Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:10.1101/gr.213462.116