qiime binary package in Ubuntu Xenial amd64
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.
Publishing history
Date | Status | Target | Component | Section | Priority | Phased updates | Version | ||
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2016-04-08 00:10:13 UTC | Deleted | Ubuntu Xenial amd64 | proposed | universe | science | Extra | 1.9.1+dfsg-1 | ||
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2015-10-22 15:20:22 UTC | Published | Ubuntu Xenial amd64 | release | universe | science | Extra | 1.8.0+dfsg-4 | ||
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