phu 0.2.0

Phage bioinformatics utilities (seqclust runner and friends).

phu

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phu (phage utilities) or phutilities, is a modular toolkit for viral genomics workflows. It provides command-line tools to handle common steps in phage bioinformatics pipelines—wrapping complex utilities behind a consistent and intuitive interface.

Installation

[!WARNING] phu is currently in the process of being published on Bioconda. The package may not be immediately available. Please check back soon or follow this repository for updates.

phu will be available through Bioconda. To install (once available), use the following command:

mamba create -n phu bioconda::phu

Meanwhile you can install phutilities using pip in an a custom conda/mamba environment with the current software requirments:

mamba create -n phu -c bioconda seqkit vclust 
mamba activate phu
python -m pip install phu

Usage

phu <command> [options]

Commands

• cluster: Cluster viral sequences into species or other operational taxonomic units (OTUs).

Contributing

We welcome contributions to phu! Please follow these steps:

1. Fork the repository.
2. Create a new branch for your feature or bugfix.
3. Make your changes and commit them.
4. Submit a pull request describing your changes.