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Additional information
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    :Version: |version|
    :Date: |today|
    

.. contents::

.. _background:

Project Status
==============

The project is available on `GitHub <https://github.com/JFsanchezherrero/BacterialTyper>`_. You can 
`report issues <https://github.com/JFsanchezherrero/BacterialTyper/issues>`_ or contribute to the project by 
`forking the project <https://help.github.com/en/github/getting-started-with-github/fork-a-repo>`_
and `creating pull requests <https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests>`_. 
See additional details on BacterialTyper :ref:`developer guidelines<developer>` and how to :ref:`work with Git<git-guidelines>`.


Background
==========

*Staphylococcus aureus* is a major bacterial pathogen causing a variety of diseases ranging from wound infections to 
severe bacteremia or intoxications. Besides host factors, the course and severity of disease is also widely dependent 
on the genotype of the  bacterium :cite:`Straus2016`. Whole-genome sequencing (WGS) and the following bioinformatic 
sequence analysis, is the most extensive genotyping method available but neither open, easy, direct and straighforward 
analysis are available that provide researchers with integrative genotyping information.

The ``BacterialTyper`` pipeline started as a collaboration with Dra. Cristina Prat and Dra. Alicia Lacoma to asses the
genotyping characteristics of a set of *S. aureus* samples.  


.. _license:

License
=======

This is brief description of the license terms for ``BacterialTyper``. 


.. _credits:

Credits
=======

Give credit to who deserves


.. _citation:

Citation
========

Please cite the ``BacterialTyper`` project, code or documentation using the following links:

.. github_stats:

Github statistics
=================

These are Github statistics generated for each release of the code.

.. include:: ./github_stats.txt
   :literal:

.. _whats_new:

What's new?
===========

See below information on differences among each release of the code generated.

.. include:: ./whats_new.txt
   :literal:
  
 
.. include:: ../links.inc