.. title:: API guide

API Overview
------------
.. toctree::
   :hidden:
   
   BacterialTyper.rst
   modules/modules_index.rst
   scripts/scripts_index.rst
   other_tools.rst
   data.rst
   third_party.rst
   

.. only:: html

    :Version: |version|
    :Date: |today|

Here we include and API_ documentation for ``BacterialTyper`` in order to provide third parties to use the 
functionality of ``BacterialTyper`` application

This pipeline is composed of multiple modules and scripts that are separated in a main script:

- ``BacterialTyper.py``

This main script integrates and connects all available modules and analysis arranged in 
several directories:

- ``BacterialTyper/modules``
- ``BacterialTyper/scripts``
- ``BacterialTyper/data``
- ``BacterialTyper/other_tools``
- ``BacterialTyper/config``


Additionally, we include a third-party software named IslandPath-DIMOB. See additional 
details in section: :ref:`IslandPath-DIMOB forked version<islandPath-DIMOB-forked>`.

- ``third_party/IslandPath-DIMOB``

Contents
^^^^^^^^

.. toctree::
   :maxdepth: 2

   BacterialTyper.rst
   modules/modules_index.rst
   scripts/scripts_index.rst
   config/config_index.rst
   other_tools.rst
   data.rst
   third_party.rst
   
 
.. ############ 
.. include:: ../links.inc