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:

• vConTACT3 version
• vConTACT3 prepare_databases
• vConTACT3 run