.. MARIO documentation master file, created by
   sphinx-quickstart on Thu Jan 14 14:06:45 2016.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to MARIO-tools's documentation!
=======================================

Contents:

.. toctree::
   :maxdepth: 3
   
   MARIO

   Analysis_pipeline

   Visualization.rst

   Other_api.rst
  
   Data_Resources

.. note::

   MARIO-tools benifits a lot from BAM2X, a convenient python interface for most common NGS datatypes. `Try BAM2X now <http://www.bam2x.net/>`_!


Updates
-------


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


Supplementary methods
=====================

:download:`MARIO-tools-online-methods.pdf <MARIO-tools-online-methods.pdf>`


Archived pipeline
=================