Skip to main content

Useful additions to the QIIME analysis pipeline including tools for data visualization and cluster-computing.

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The QIIME-tools project is now obsolete and has been replaced by PhyloToAST.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

Latest Version https://pypip.in/d/qiime-tools/badge.svg License Download format

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

qiime-tools-1.1.2.tar.gz (32.4 kB view hashes)

Uploaded source

Built Distribution

qiime_tools-1.1.2-py2.py3-none-any.whl (45.2 kB view hashes)

Uploaded 2 7

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page