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Title: QIIME: Quantitative Insights Into Microbial Ecology
Author: Greg Caporaso <gregcaporaso@gmail.com>
Abstract: 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.
.
Rather than reimplementing commonly used algorithms, QIIME wraps popular
implementations of those algorithms. This allows us to make use of the
many excellent tools available in this area, and allows faster
integration of new tools. If you use tools that you think would be
useful additions to QIIME, consider submitting a feature request.
.
A standard QIIME analysis begins with sequence data from one or more
sequencing platforms, including Sanger, Roche/454, and Illumina GAIIx.
QIIME can perform library de-multiplexing and quality filtering;
denoising with AmpliconNoise or the QIIME Denoiser; 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 area, bar and
pie charts along with distance histograms; and many other features.
While QIIME is primarily used for analysis of amplicon data, many of the
downstream analysis pipeline (such as alpha rarefaction and jackknifed
beta diversity) can be performed on any type of sample x observation
tables if they are formatted correctly.
Section: Science/Biology
Format: html
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