Metadata-Version: 1.1
Name: qiime-default-reference
Version: 0.1.2
Summary: Default reference data files for use with QIIME.
Home-page: http://www.qiime.org
Author: QIIME development team
Author-email: qiime.help@gmail.com
License: CC BY-SA 3.0
Description: qiime-default-reference
        -----------------------
        
        |Build Status| |Coverage Status|
        
        qiime-default-reference, canonically pronounced *chime default reference*, is a
        Python package containing default reference data files for use with
        `QIIME <http://qiime.org/>`_. The current default reference data is compiled
        from the Greengenes 16S rRNA database version
        `13_8 <ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz>`_.
        Please see the **Attribution** section below for more details.
        
        Installation
        ------------
        To install qiime-default-reference::
        
            pip install qiime-default-reference
        
        Running the tests
        -----------------
        To run qiime-default-reference's unit tests::
        
            nosetests --with-doctest qiime_default_reference
        
        Attribution
        ^^^^^^^^^^^
        The reference data distributed in this Python package were copied from the
        `Greengenes 16S rRNA database <http://greengenes.secondgenome.com/>`_:
        
        **An improved Greengenes taxonomy with explicit ranks for ecological and
        evolutionary analyses of bacteria and archaea.**
        McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A,
        Andersen GL, Knight R, Hugenholtz P.
        ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139.
        
        The Greengenes reference data is licensed under a
        `Creative Commons Attribution-ShareAlike 3.0 Unported License <http://creativecommons.org/licenses/by-sa/3.0/deed.en_US>`_.
        
        The default template alignment column mask (i.e., "Lane mask") is derived from:
        
        Lane,D.J. (1991) **16S/23S rRNA sequencing.** In Stackebrandt,E. and
        Goodfellow,M. (eds), Nucleic Acid Techniques in Bacterial Systematics.
        John Wiley and Sons, New York, pp. 115-175.
        
        Lane mask was originally available in `ARB <http://www.ncbi.nlm.nih.gov/pubmed/14985472>`_.
        
        Lane mask taken from `here <http://greengenes.lbl.gov/Download/Sequence_Data/lanemask_in_1s_and_0s>`_.
        
        Getting Help
        ^^^^^^^^^^^^
        Please post your questions about this repository/package on the `QIIME Forum <http://forum.qiime.org>`_.
        
        .. |Build Status| image:: https://travis-ci.org/biocore/qiime-default-reference.svg?branch=master
           :target: https://travis-ci.org/biocore/qiime-default-reference
        .. |Coverage Status| image:: https://coveralls.io/repos/biocore/qiime-default-reference/badge.png
           :target: https://coveralls.io/r/biocore/qiime-default-reference
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
