QIIME 1.5
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QIIME 1.5
General Introduction
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.
QIIME 1.5 installation files (edited for installation on Cheaha cluster) are located at /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0
QIIME 1.5 program is located at /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/
QIIME Tutorial
Installation steps for Cheaha cluster
This installation is based on QIIME installation script for Ubuntu.
- Make sure no external module is loaded (for avoiding any conflicts)
- Downloading the QIIME
<source lang="csharp">wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz tar zxvf app-deploy-qiime-1.5.0.tgz </source>
- Editing the configuration file