HP-PBWT

Haplotype-based parallel PBWT.

For questions regarding the method, extensions, or potential research use, please contact the corresponding author, Kecong Tang (Kecong.Tang@ucf.edu or Benjamin.KT.vln@gmail.com).

HP-PBWT is a tool to parallel Durbin's PBWT's all vs all L-Long Matches and Set-Maximal Matches by dividing the haplotype dimension. More detailed information will be provided later.

Durbin's PBWT can be found at https://github.com/richarddurbin/pbwt.

Source Code files for general purposes can be found in source_IO_Included/

Source Code files for IO-Excluded bencharmk can be found in source_IO_Excluded/

Dependencies

Compile and run C#:

1. Install .NET SDK:

   For Winodows:

   Follow instructions from https://learn.microsoft.com/en-us/dotnet/core/install/windows

   For Linux:

   sudo apt-get update

   sudo apt-get install -y dotnet-sdk-8.0

   Addational details could be found at https://learn.microsoft.com/en-us/dotnet/core/install/linux-ubuntu-install?tabs=dotnet9&pivots=os-linux-ubuntu-2410

2. Build:

   a. Create a directory (E.g. HP-PBWT).

   b. Download all the files from the source directory (source_IO_Included/ or source_IO_Excluded/) to the directory created in a.

   c. Run "dotnet build --configuration Release" in the directory

3. Run:

   The compiled executable file should be /bin/Release/net8.0/HP-PBWT

   The directory name depends on the dotnet version, "net8.0" for dotnet 8.0.

Citation

The HP-PBWT method was formally published in the proceedings of ICCABS 2025.

Official publication:

Kecong Tang, Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang.

Haplotype-based Parallel PBWT for Biobank Scale Data.

In Computational Advances in Bio and Medical Sciences, 13th International Conference (ICCABS 2025), Revised Selected Papers. Springer Nature, 2025.

DOI: https://doi.org/10.1007/978-3-032-02489-3_10

@inproceedings{Tang2025HPPBWT,
  author    = {Tang, Kecong and Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title     = {Haplotype-Based Parallel PBWT for Biobank Scale Data},
  booktitle = {Computational Advances in Bio and Medical Sciences},
  series    = {ICCABS 2025, Revised Selected Papers},
  year      = {2025},
  publisher = {Springer Nature},
  doi       = {10.1007/978-3-032-02489-3_10}
}

A preprint version of this work was previously available on bioRxiv (2025).