phu 0.3.0

Phage bioinformatics utilities (seqclust runner and friends).

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phu - Phage Utilities

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

You can install phu using mamba or conda from the bioconda channel:

mamba create -n phu bioconda::phu

Usage

As a command-line tool, phu follows a modular structure. You can access different functionalities through subcommands. The general syntax is:

phu <command> [options]

Commands

• cluster: Cluster viral sequences into species or other operational taxonomic units (OTUs).
• simplify-taxa: Simplify vContact taxonomy prediction columns into compact lineage codes.

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.

Developers

You can also install the development version of phu directly from GitHub:

git clone https://github.com/camilogarciabotero/phu.git
cd phu
pip install -e .

phu is also available on PyPI:

pip install phu

References

This program uses several key tools and libraries, make sure to acknowledge them when using phu:

• vclust: A high-performance clustering tool for viral sequences:

Zielezinski A, Gudyś A, Barylski J, Siminski K, Rozwalak P, Dutilh BE, Deorowicz S. Ultrafast and accurate sequence alignment and clustering of viral genomes. Nat Methods. https://doi.org/10.1038/s41592-025-02701-7

• seqkit: A toolkit for FASTA/Q file manipulation.

Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.