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.