PhageMine: Bacteriophage Genome Annotation and Comparative Genomics

PhageMine is an open-source bioinformatics pipeline for bacteriophage genome annotation, functional evidence integration and comparative genomics. It combines phage-focused gene prediction with protein sequence and profile searches, links functional assignments to their supporting evidence, and produces annotated sequences, evidence tables and an HTML report.

PhageMine uses PHANOTATE for protein-coding gene prediction; PHROGs, VOGDB, Pfam and Swiss-Prot for functional evidence; and INPHARED references for comparative genomic context. It is designed for researchers working in phage genomics, bacteriophage genome annotation, viral genomics and related bioinformatics workflows.

What it does

• Predicts protein-coding genes with PHANOTATE.
• Uses PHROGs, VOGDB, Pfam and Swiss-Prot to assess protein function.
• Reports supporting evidence, conflicting assignments and unknown functions.
• Processes individual genomes or genome collections.
• Groups related proteins into families and compares genomes with INPHARED references.
• Exports GFF3, protein FASTA and GenBank preparation files.

Install

The current stable release is v1.3.1. Python 3.10 or later is required.

Install from Bioconda, which brings the external analysis tools with it:

conda create --name phagemine --channel conda-forge --channel bioconda phagemine
conda activate phagemine
phagemine doctor

Or from PyPI, with the external tools installed separately:

pip install phagemine

To install from source instead:

git clone --branch v1.3.1 --depth 1 https://github.com/emmannaemeka/PhageMine.git
cd PhageMine
conda env create --file environment.yml
conda activate phagemine
python -m pip install .
phagemine doctor

Install the databases before running functional annotation:

phagemine databases install --all

This installs PHROGs, Swiss-Prot, Pfam and VOGDB, plus PMFDB and INPHARED comparative references. Prepared databases require additional disk space beyond the download sizes.

See the installation guide for platform requirements and troubleshooting.

Annotate a genome

Supply a single-genome nucleotide FASTA file:

phagemine run genome.fasta --output results/genome --threads 8

Open results/genome/report.html to browse the results. The output directory also contains annotation.tsv, genes.gff3, proteins.faa and supporting evidence files.

To check the installation with the bundled example:

phagemine run examples/demo_phage.fasta --output results/example

Installed databases are detected automatically. Without them, the example checks gene prediction and report generation; functional evidence is unavailable.

Run phagemine --help for all commands and phagemine run --help for annotation options.

Reading the results

Product names describe the function supported by the available evidence. Proteins without a supported function remain hypothetical or are identified as conserved proteins of unknown function. Gene symbols, protein products and locus identifiers are reported separately.

PhageMine is research software. Functional predictions require review, and confidence labels describe evidence strength rather than calibrated probabilities. See the limitations for interpretation.

Citation and support

Citation information is available in CITATION.cff and the archived release.

Report bugs or request features through GitHub Issues. PhageMine is distributed under the MIT licence.