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Project Description

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The QIIME-tools project is now obsolete and has been replaced by PhyloToAST.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

Release History

Release History

1.1.2

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.1.1

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TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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1.1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
qiime_tools-1.1.2-py2.py3-none-any.whl (45.2 kB) Copy SHA256 Checksum SHA256 2.7 Wheel Sep 19, 2014
qiime-tools-1.1.2.tar.gz (32.4 kB) Copy SHA256 Checksum SHA256 Source Sep 19, 2014

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