Welcome to PhyloToAST documentation! ==================================== The PhyloToAST project is a collection of python scripts that modifies the original QIIME [1]_ pipeline: .. figure:: figures/qiime-pipeline.png :scale: 45 % :align: center by adding or modifying several steps (as seen below) including support for PBS-based cluster-computing, multiple primer support [2]_, enhanced support for species-specific analysis, and additional visualization tools. .. figure:: figures/phylotoast-pipeline.png :scale: 45 % :align: center Download and install PhyloToAST_ package. .. _PhyloToAST: https://pypi.python.org/pypi/qiime-tools/1.1.2 PhyloToAST Scripts ================== .. toctree:: :maxdepth: 1 scripts/api.txt scripts/other.txt scripts/visualization.txt Citations: .. [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 `_ .. [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 `_ Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`