vConTACT3 run
=============

The `run` subcommand performs viral genome clustering and taxonomic assignment using nucleotide or protein inputs.

Usage Examples:
---------------

Run with nucleotide input:

.. code-block:: bash

   vcontact3 run --nucleotide genomes.fna --output results_dir

Run with pre-predicted protein inputs:

.. code-block:: bash

   vcontact3 run --proteins proteins.faa --gene2genome gene2genome.tsv --len-nucleotide genome_lengths.tsv --output results_dir

Customize database domain and exports:

.. code-block:: bash

   vcontact3 run --nucleotide genomes.fna --db-domain prokaryotes --exports graphml d3js completeness --output results_dir

Command Line Reference:
-----------------------

.. argparse::
   :module: vcontact3.cli
   :func: build_parser
   :prog: vcontact3 run
   :nosubcommands: