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HapCUT2 website  

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

Environment Modules

Run module spider HapCUT2 to find out what environment modules are available for this application.

System Variables

  • HPC_HAPCUT2_DIR - installation directory
  • HPC_HAPCUT2_BIN - executable directory


If you publish research that uses HapCUT2 you have to cite it as follows:

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