vConTACT3 Documentation

Welcome to the documentation for vConTACT3 — a viral genome clustering and taxonomic assignment tool.

vConTACT3 is the latest iteration in the vConTACT family. Each version improves upon the foundational philosophy: more related virus genomes should share more genes - Viral CONTig Automatic Clustering and Taxonomy.

vConTACT3 is faster, more scalable, more accurate, and features more outputs than prior versions. Databases are now handled more efficiently and are more portable than before.

Contents:

User Guide

• Installation
• Quickstart
• Command Line Interface (CLI)
• Examples and Workflows
• FAQ & Troubleshooting

Inputs & Outputs

• Inputs & Parameters
• Results & Reports
• The Final Assignments File
• Exports
• Graph-based Outputs
• Cluster Profiles
• ANI-based genome similarities
• Other Outputs

Databases

• Databases

Performance & Optimization

• Memory Usage & Performance Considerations

About & Citations

• Citations & Acknowledgements
• Release Notes
• Future Work