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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.

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HapCUT classification

HapCUT specifications

Software type:
Restrictions to use:
Input format:
Operating system:
Command line interface
Input data:
A file for an individual containing reads aligned to a reference genome and a file containing SNVs for the individual with respect to the reference.
Output data:
It outputs the phased haplotype blocks that can be assembled from the sequence reads.
Computer skills:

HapCUT distribution


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HapCUT support



  • Vikas Bansal <>
  • Vikas Bansal <>

Additional information

Previous version:


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Department of Computer Science & Engineering, University of California, San Diego, La Jolla CA, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA

Funding source(s)

Supported in part by a grant from the NIH (HG007430, HG007836 and GM114362) and NSF (DBI-1458557, IIS-1318386).

Link to literature

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