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The QIIME-tools project is now obsolete and has been replaced by PhyloToAST.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-toolsFrom source:
$ python setup.py installDocumentation
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
1 maintainer
Metadata
1 maintainer
Release files for qiime-tools 1.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| qiime-tools-1.1.2.tar.gz | 32.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| qiime_tools-1.1.2-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details |
Total release size: 77.6 kB
Release files / qiime-tools-1.1.2.tar.gz
| Download URL | qiime-tools-1.1.2.tar.gz |
|---|---|
| Size | 32.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
fad37c85e576b17448f7b7998b08793429460e1a66ff052df03c2c43751fa911
|
|
BLAKE2b-256 checksum How to use checksums |
4b99e2df83152a22a5cc67ac8aad09f06d695587c858bef35bc2a15173f1eabf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Release files / qiime_tools-1.1.2-py2.py3-none-any.whl
| Download URL | qiime_tools-1.1.2-py2.py3-none-any.whl |
|---|---|
| Size | 45.2 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
3224203968a59ef6fd71781254a2f6132b209848f190b1b19c3fa96eafa2a95c
|
|
BLAKE2b-256 checksum How to use checksums |
15426c589eaffb68e326e3a098660a9cbbe2504932d341b55869c34a21be3449
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
