.. bcbio_nextgen documentation master file, created by
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.. image:: contents/images/github.png
   :alt: bcbio banner
   :align: center

A python toolkit providing best-practice pipelines for fully automated
high throughput sequencing analysis. You write a high level
configuration file specifying your inputs and analysis parameters.
This input drives a parallel pipeline that handles distributed
execution, idempotent processing restarts and safe transactional
steps. The goal is to provide a shared community resource that handles
the data processing component of sequencing analysis, providing
researchers with more time to focus on the downstream biology.

Contents:

.. toctree::
   :maxdepth: 2

   contents/introduction
   contents/installation
   contents/pipelines
   contents/testing
   contents/configuration
   contents/parallel
   contents/cwl
   contents/cloud
   contents/outputs
   contents/code
   contents/internals
   contents/presentations
   contents/teaching
   contents/citations


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

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