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hapdup website  

HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The reconstructed haplotypes preserve heterozygous structural variants (in addition to small variants) and are locally phased.

Environment Modules

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

System Variables

  • HPC_HAPDUP_DIR - installation directory
  • HPC_HAPDUP_BIN - executable directory


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

Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Gunjan Baid et al. "Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks." bioRxiv (2021). doi:10.1101/2021.03.04.433952

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8