.. MetaSUB CAP documentation master file, created by
   sphinx-quickstart on Fri Oct 30 10:34:55 2020.
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The MetaSUB Core Analysis Pipeline
==================================

The MetaSUB Core Analysis Pipeline is a python package for metagenomic analysis. It's a consistent interface over a complex pipeline making it easy to build more complex analyses. It's the core set of tools that should be run on every metagenome. It's highly reproducible and extendable.

It aims to take the drudgery out of analyzing microbiomes while making complex analyses easy.

The CAP in three points:

- best practice quality control and analysis
- highly reproducible scientific analyses
- consistent, extensible, interface

Source Code may be found on GitHub `here <https://github.com/MetaSUB/CAP2>`_.

.. toctree::
   :maxdepth: 2
   :caption: Documentation:

   Quickstart <quickstart>
   Architecture and Design <architecture>
   Pipeline modules <modules>
   Creating and Parsing Data Tables <capalyzer>
   API Reference <api>
   Citing the CAP <citation>
   License <license>



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

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