1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
Source: qiime
Section: science
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Tim Booth <tbooth@ceh.ac.uk>,
Andreas Tille <tille@debian.org>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), python-cogent ( >= 1.5.1 ),
python-numpy, python-matplotlib, ghc6, python-sphinx
Standards-Version: 3.9.3
Homepage: http://www.qiime.org/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qiime/trunk/
XS-Python-Version: >= 2.6
Package: qiime
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 )
Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal,
fasttree, ampliconnoise, python-matplotlib, python-numpy
Suggests: t-coffee, cytoscape
Replaces: denoiser
Conflicts: denoiser
Provides: denoiser
XB-Python-Version: ${python:Versions}
Description: Quantitative Insights Into Microbial Ecology
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
microbial community analysis that integrates many third party tools which
have become standard in the field. A standard QIIME analysis begins with
sequence data from one or more sequencing platforms, including
* Sanger,
* Roche/454, and
* Illumina GAIIx.
With all the underlying tools installed,
of which not all are yet available in Debian (or any other Linux
distribution), QIIME can perform
* library de-multiplexing and quality filtering;
* denoising with PyroNoise;
* OTU and representative set picking with uclust, cdhit, mothur, BLAST,
or other tools;
* taxonomy assignment with BLAST or the RDP classifier;
* sequence alignment with PyNAST, muscle, infernal, or other tools;
* phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
* alpha diversity and rarefaction, including visualization of results,
using over 20 metrics including Phylogenetic Diversity, chao1, and
observed species;
* beta diversity and rarefaction, including visualization of results,
using over 25 metrics including weighted and unweighted UniFrac,
Euclidean distance, and Bray-Curtis;
* summarization and visualization of taxonomic composition of samples
using pie charts and histograms
and many other features.
.
QIIME includes parallelization capabilities for many of the
computationally intensive steps. By default, these are configured to
utilize a mutli-core environment, and are easily configured to run in
a cluster environment. QIIME is built in Python using the open-source
PyCogent toolkit. It makes extensive use of unit tests, and is highly
modular to facilitate custom analyses.
Package: qiime-doc
Section: doc
Architecture: all
Depends: ${misc:Depends}, libjs-jquery, libjs-underscore
Description: Quantitative Insights Into Microbial Ecology (tutorial)
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
microbial community analysis that integrates many third party tools which
have become standard in the field. A standard QIIME analysis begins with
sequence data from one or more sequencing platforms, including
* Sanger,
* Roche/454, and
* Illumina GAIIx.
With all the underlying tools installed,
of which not all are yet available in Debian (or any other Linux
distribution), QIIME can perform
* library de-multiplexing and quality filtering;
* denoising with PyroNoise;
* OTU and representative set picking with uclust, cdhit, mothur, BLAST,
or other tools;
* taxonomy assignment with BLAST or the RDP classifier;
* sequence alignment with PyNAST, muscle, infernal, or other tools;
* phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
* alpha diversity and rarefaction, including visualization of results,
using over 20 metrics including Phylogenetic Diversity, chao1, and
observed species;
* beta diversity and rarefaction, including visualization of results,
using over 25 metrics including weighted and unweighted UniFrac,
Euclidean distance, and Bray-Curtis;
* summarization and visualization of taxonomic composition of samples
using pie charts and histograms
and many other features.
.
QIIME includes parallelization capabilities for many of the
computationally intensive steps. By default, these are configured to
utilize a mutli-core environment, and are easily configured to run in
a cluster environment. QIIME is built in Python using the open-source
PyCogent toolkit. It makes extensive use of unit tests, and is highly
modular to facilitate custom analyses.
.
This package contains the documentation and a tutorial.
|
