Qiime

QIIME (http://qiime.org/) (canonically 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 studies based on billions of sequences from thousands of samples.

On N3phele, we provide the option to run various QIIME scripts as jobs or services. Some of the supported operations include creating an virtual machine with the latest QIIME version and the denoising of 454 data sets. N3phele also has a generator module (nshell-generator) that can produce nshell scripts from any QIIME script, facilitating their usage in the N3phele environment.