.. breseq documentation master file, created by
   sphinx-quickstart on Wed Sep  8 19:51:44 2010.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

========================
:program:`breseq` Manual
========================

Contents:

.. toctree::
   :maxdepth: 3

   Introduction <introduction>
   Installation <installation>
   Usage Summary <usage>
   Test Drive <test_drive>
   Methods <methods>
   Output <output>
   References <references>
   Acknowledgments <acknowledgments>

Tutorials:

.. toctree::
   :maxdepth: 1

   Tutorial 1: Clonal Samples <tutorial_clones>
   Tutorial 2: Mixed Populations <tutorial_populations>
   Tutorial 3: Consensus Reads and Targeted Sequencing <tutorial_barcoded_targeted>

Appendices:

.. toctree::
   :maxdepth: 1

   Frequently Asked Questions (FAQ) <faq>
   gdtools Utility <gd_usage>
   Genome Diff Format <gd_format>
   Reference Sequence Format <refseq_format>

Documentation last updated |today|\ .

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

.. * :ref:`genindex`
.. * :ref:`search`