HyperGen.jl (under development)

Compact and Efficient Genome Sketching using Hyperdimensional Vectors (in Julia).

Table of Contents

• Installation
• Usage
• Support
• Contributing

Installation

To install HyperGen.jl, clone the repository and run the following:

git clone https://github.com/cvigilv/HyperGen.jl
make install

Additionally, you can install the package directly from Julia's REPL:

using Pkg
Pkg.add(url="git://github.com/cvigilv/HyperGen.jl.git")

Usage

CLI

After running the installation steps, you can use the hypergenjl command in your terminal.

Run the following command to see available options:

$ hypergen --help
HyperGen.jl  - v0.1.0
usage: hypergenjl [-V] [-h] {sketch|compare|combine|search|tree}

Compact and Efficient Genome Sketching using Hyperdimensional Vectors (in Julia)

commands:
  sketch         Sketch sequences into hypervectors
  compare        Compare sketches hypervectors
  combine        Combine sketches hypervectors
  search         Search sequences in sketch hypervectors
  tree           Compute phylogenetic tree from distance / ANI matrix

optional arguments:
  -V, --verbose  Increase verbosity of program
  -h, --help     show this help message and exit

Copyright (C) 2025 Carlos Vigil-Vásquez (carlos.vigil.v@gmail.com). Permission
to copy and modify is granted under the MIT license

Julia API

You can also use HyperGen.jl as a Julia package. Here is a simple example of how to sketch a sequence:

Under construction

Support

Please open an issue for support.

Contributing

Please contribute using Github Flow. Create a branch, add commits, and open a pull request.

The repo contains a Makefile with multiple targets useful for testing and developing the package. To see all available targets, run:

make help

of simply,

make

Acknowledgements

This work was supported by Universite de Lille and the EGBSL, in conjunction with the IPL, University of Ghent and the KERMIT research group.

Citation

If you use HyperGen.jl in your research, please cite the following paper:

• Weihong Xu, Po-Kai Hsu, Niema Moshiri, Shimeng Yu, Tajana Rosing, HyperGen: compact and efficient genome sketching using hyperdimensional vectors, Bioinformatics, Volume 40, Issue 7, July 2024, btae452, https://doi.org/10.1093/bioinformatics/btae452

License

MIT License - Refer to [[LICENSE]] for more information