Bug#587275: ITP: qiime -- Quantitative Insights Into Microbial Ecology
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>
* Package name : qiime
Version : 1.1.0
* URL : http://qiime.sf.net
* License : GPL
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.
Reply to: