Difference between revisions of "QIIME"
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Revision as of 16:33, 10 August 2012
Description
QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.
Execution Environment and Modules
To use qiime with the environment modules system at HPC the following commands are available:
Get module information for qiime:
$module spider qiime
Load the default application module:
$module load qiime
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_QIIME_DIR - directory where qiime is located.