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.
