qiime-tools 1.1.2

Description:

qiimetools 1.1.2

NOTICE
The QIIME-tools project is now obsolete and has been
replaced by PhyloToAST. The new project is available on GitHub and
on PyPI. PhyloToAST can be installed with pip:

$ pip install phylotoast



QIIME-tools




The QIIME-tools project is a collection of python code and scripts that
modify the original QIIME [1] pipeline by adding/changing several
steps including: support for cluster-computing, multiple primer support
(eliminate primer bias) [2], enhanced support for species-specific
analysis, and additional visualization tools.

Installation
To install QIIME-tools from PyPI:
$ pip install qiime-tools
From source:
$ python setup.py install


Documentation
Full documentation for the scripts and code is available at the
QIIME-tools documentation site


Requirements
matplotlib for PCoA plots. Biopython for some sequence and fastq
processing, although its use is being phased out. fuzzpy for the
otu_calc module. Note that these are not listed as dependencies in the install
script because they are not required for all functionality. Install as needed.


Source
The QIIME-tools source is hosted on github.


Citing
A manuscript describing the qiime-tools software is currently in
preparation. Until publication, please cite the github repository and
the author: Shareef M. Dabdoub.


Publications using QIIME-tools
Mason et al., The subgingival microbiome of clinically healthy current
and never smokers. The ISME Journal, 2014; doi:10.1038/ismej.2014.114
Dabdoub et al., Patient-specific Analysis of Periodontal and Peri-implant Microbiomes.
Journal of Dental Research, 2013; doi: 10.1177/0022034513504950


References
[1] J Gregory Caporaso, et al., QIIME allows analysis of
high-throughput community sequencing data. Nature Methods, 2010;
doi:10.1038/nmeth.f.303
[2] Kumar PS, et al., Target Region Selection Is a Critical Determinant
of Community Fingerprints Generated by 16S Pyrosequencing. PLoS ONE
(2011) 6(6): e20956. doi:10.1371/journal.pone.0020956