Command Line Interface (CLI)
============================

vConTACT3 provides a command-line interface with three primary subcommands:

- **version**: Print the current vConTACT3 version and exit.
- **prepare_databases**: Download and set up reference databases for analysis.
- **run**: Perform viral genome clustering and taxonomic assignment.

Each subcommand has its own documentation page with usage examples and detailed options.

CLI Subcommands:
----------------

.. toctree::
   :maxdepth: 1

   version
   prepare_databases
   run