Phorager

Prophage Analysis Pipeline

A comprehensive pipeline for bacterial genome quality control, prophage detection, and prophage characterization

Authors:

• Xena Dyball
• James Docherty
• Alise Ponsero
• Ryan Cook

Citation: [Paper Citation or Preprint Link]

Overview

Phorager provides an integrated workflow for:

• Bacterial genome quality control - CheckM2 assessment, filtering, and dRep dereplication
• Prophage detection - GenoMAD and VIBRANT-based identification of integrated prophages
• Phage annotation - CheckV quality assessment, Pharokka annotation, and Phold function prediction
• Summary tables - Structured TSV summaries of QC metrics and prophage characteristics across your dataset

Note: Phorager is currently in beta release. We welcome feedback, bug reports, and feature requests through our issue tracker.

Quick Start

1. Configure

Set your preferred installation backend and locations:

phorager config set --backend conda --db-location /data/phorager

2. Install

Install required tools and databases:

# Install tools for bacterial genome analysis
phorager install --tools genome --databases checkm2

# Install prophage detection tools
phorager install --tools prophage --databases genomad,vibrant

3. Run Analysis

Execute workflows on your data:

# Bacterial genome quality control
phorager bacterial --genome /path/to/genomes --outdir results/

# Prophage detection
phorager prophage --genome /path/to/genomes --outdir results/

# Prophage annotation and clustering
phorager annotation --prophage results/ --outdir results/

4. Generate Summaries

Create structured summary tables from your completed results:

# Bacterial genome QC metrics with prophage counts
phorager summarize --type bacterial_genome --outdir results/

# Per-prophage table with host, cluster, quality, and annotation
phorager summarize --type prophage_table --outdir results/

Output is written to results/4.Summaries/. Use phorager summarize --list to see all available summary types.

Prerequisites

• Nextflow (≥ 21.04.0)
• Either Conda/Mamba or Singularity

Documentation

For detailed documentation, see the Wiki:

• Configuration - Backend setup and locations
• Installation - Tools and database installation
• Bacterial Workflow - Genome quality control and dereplication
• Prophage Workflow - Integrated prophage detection
• Annotation Workflow - Prophage annotation and clustering
• Summary Workflow - Generating summary tables from pipeline outputs

Getting Help

• Check command-specific help: phorager [command] --help
• View available tools and databases: phorager install --list-available
• Preview commands before running: phorager [command] --dry-run
• See current configuration: phorager config show
• List available summary types: phorager summarize --list

Reporting Issues and Feedback

Phorager is actively being developed and improved. We encourage users to:

• Report bugs - Found an issue? Open a bug report
• Request features - Have an idea for improvement? Submit a feature request
• Ask questions - Need help? Start a discussion
• Share feedback - Let us know about your experience using Phorager

When reporting issues, please include:

• Command used
• Error messages or unexpected behavior
• Phorager version and backend (conda/singularity)
• System information (OS, available resources)