RLSRP_2025

This is the GitHub repository containing all code for the preprint
Reference-based variant detection with varseek
by Joseph Matthew Rich, Laura Luebbert, Delaney Sullivan, Reginaldo Rosa, and Lior Pachter.

Preprint: Reference-based variant detection with varseek

varseek: GitHub - pachterlab/varseek

Examples for getting started: GitHub - pachterlab/varseek-examples

Getting Started

To run the code in this repository, follow these steps:

git clone https://github.com/pachterlab/RLSRP_2025.git
cd RLSRP_2025

We recommend using an environment manager such as conda. Some additional non-python packages must be installed for full functionality. If using conda (recommended), simply run the following:

conda env create -f environment.yml
conda activate RLSRP_2025

Otherwise, install these packages manually as-needed (see environment.yml for the list of packages and recommended versions).

Once the environment is set up, install the repository as a package.

pip install .

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Repository Contents

notebook/: Jupyter notebooks to reproduce each main and supplemental figure, named according to the figure number. RLSRP_2025/: Core functions used within notebooks scripts/: Long scripts for generating variant indices or running variant calling with varseek and other tools

License

This project is licensed under the BSD 2-Clause License. See the LICENSE file for details.

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For any issues or contributions, feel free to open a pull request or issue in this repository.