AVrC Toolkit

AVrC Toolkit

A Python package for downloading and filtering sequences from the Aggregated Gut Viral Catalogue (AVrC).

Overview

The AVrC Toolkit provides command-line utilities to:

• Download complete or subset data from the AVrC database
• Filter sequences based on quality metrics, taxonomy, and host information
• Extract specific viral groups for analysis

Data Source

The AVrC dataset is available through Zenodo: https://doi.org/10.5281/zenodo.11426065

Quick Links

• Complete Documentation - Comprehensive wiki with tutorials and reference guides
• Installation Guide - Detailed setup instructions
• Command Reference - Complete command documentation
• Tutorials - Step-by-step guides and examples

Quick Start

# Install the toolkit
pip install git+https://github.com/aponsero/AVrC_toolkit.git

# List available datasets
avrc download --list

# Download high-quality subset
avrc download hq -o data/

# Filter for specific viral groups
avrc filter data/ --host-phylum Firmicutes --output both

Citation

If you use this toolkit or the AVrC dataset in your research, please cite:

Galperina, A., Lugli, G. A., Milani, C., De Vos, W. M., Ventura, M., Salonen, A., Hurwitz, B., & Ponsero, A. J. (2024). The Aggregated Gut Viral Catalogue (AVrC): A Unified Resource for Exploring the Viral Diversity of the Human Gut. bioRxiv. https://doi.org/10.1101/2024.06.24.600367

Issues and Support

If you encounter any issues with the AVrC or the AVrC toolkit:

1. Check the Issues page
2. Search for similar problems
3. Open a new issue with:
   • Your system information
   • Command used
   • Complete error message
   • Example data if possible