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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.

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