Useful additions to the QIIME analysis pipeline including tools for data visualization and cluster-computing.
The QIIME-tools project is now obsolete and has been replaced by PhyloToAST.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
The QIIME-tools project is a collection of python code and scripts that modify the original QIIME  pipeline by adding/changing several steps including: support for cluster-computing, multiple primer support (eliminate primer bias) , enhanced support for species-specific analysis, and additional visualization tools.
To install QIIME-tools from PyPI:
$ pip install qiime-tools
$ python setup.py install
Full documentation for the scripts and code is available at the QIIME-tools documentation site
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.
The QIIME-tools source is hosted on github.
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
 J Gregory Caporaso, et al., QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 2010; doi:10.1038/nmeth.f.303
 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
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