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Default reference data files for use with QIIME.

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qiime-default-reference, canonically pronounced chime default reference, is a Python package containing default reference data files for use with QIIME. The current default reference data is compiled from the Greengenes 16S rRNA database version 13_8. Please see the Attribution section below for more details.


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


The reference data distributed in this Python package were copied from the Greengenes 16S rRNA database:

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.

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.

Lane mask taken from here.

Getting Help

Please post your questions about this repository/package on the QIIME Forum.

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qiime-default-reference-0.1.3.tar.gz (35.2 MB view hashes)

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