Examples and Workflows
======================

Some example use cases and workflows for vConTACT3.

The "standard" run (with defaults)
----------------------------------
.. code-block:: bash

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

The "standard" run (showing defaults)
-------------------------------------
.. code-block:: bash

   vcontact3 run --nucleotide genomes.fna --output results_dir --db-domain "prokaryotes" --db-version 228 --db-path /path/to/download/location

Specifying different database versions
--------------------------------------

As mentioned elsewhere, users can specify which version of the database they wish to use, as well as the path they downloaded
the database to.

.. code-block:: bash

   vcontact3 run run --nucleotide genomes.fna --output results_dir --db-domain "prokaryotes" --db-version 228 --db-path /path/to/download/location