Welcome to PhyloToAST documentation!
====================================

The PhyloToAST project is a collection of python scripts that modifies the original QIIME [1]_ pipeline:

.. image:: figures/phylotoast-pipeline.png
   :width: 60 %
   :align: center

by adding or modifying several steps (above in red) including support for PBS-based cluster-computing, multiple primer support [2]_, enhanced support for species-specific analysis, and additional visualization tools.

.. image:: ../images/readmepic.png
   :width: 60%
   :align: center

Installation
==================

PhyloToAST_ is avaiable on the Python Package Index (PyPI), and can be easily installed with pip:

.. code-block:: bash

        $ pip install phylotoast

.. _PhyloToAST: https://pypi.python.org/pypi/phylotoast

Using PhyloToAST
==================
.. toctree::
   :maxdepth: 1

   scripts/api.txt
   scripts/data_handling.txt
   scripts/visualization.txt
   scripts/available_scripts.txt


Citing PhyloToAST
==================

Dabdoub, S. M. et al. PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets. Sci. Rep. 6, 29123, 2016; doi: `10.1038/srep29123 <http://dx.doi.org/10.1038/srep29123>`_


Publications using PhyloToAST
=============================
Paropkari, A. D. et al. *Smoking, Pregnancy and the Subgingival Microbiome*.
Sci. Rep. 6, 30388, 2016; doi: `10.1038/srep30388 <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961950/>`_

Tsigarida and Dabdoub et al., *The Influence of Smoking on the Peri-Implant
Microbiome*. Journal of Dental Research, 2015; doi: `10.1177/0022034515590581 <http://jdr.sagepub.com/content/94/9/1202.full>`_

Mason et al., *The subgingival microbiome of clinically healthy current
and never smokers*. The ISME Journal, 2014; doi: `10.1038/ismej.2014.114 <http://www.nature.com/ismej/journal/v9/n1/full/ismej2014114a.html>`_

Dabdoub et al., *Patient-specific Analysis of Periodontal and Peri-implant Microbiomes*.
Journal of Dental Research, 2013; doi: `10.1177/0022034513504950 <http://jdr.sagepub.com/content/92/12_suppl/168S.full>`_


References
==========

.. [1] **QIIME allows analysis of high-throughput community sequencing data**. J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi: `10.1038/nmeth.f.303 <http://dx.doi.org/10.1038/nmeth.f.303>`_

.. [2] **Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing**. Kumar PS, Brooker MR, Dowd SE, Camerlengo T (2011) Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing. PLoS ONE 6(6): e20956. doi: `10.1371/journal.pone.0020956 <http://dx.doi.org/10.1371/journal.pone.0020956>`_

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

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