What is QIIME? 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.
What is the QIIME VirtualBox? Because of the ‘pipeline’ nature of QIIME, there are many external dependencies and installation can therefore be a challenge. The QIIME Virtual Box should get around that problem, and is a fully functional environment for analyzing microbial community surveys and visualizing results.
The QIIME Virtual Box is a virtual machine based on Ubuntu Linux which comes pre-packaged with QIIME’s dependencies. This is the fastest way to get up-and-running with QIIME, and is useful for small analyses (approximately up to a full 454 run); and testing QIIME to determine if it meets your needs before investing time in installing it, for example, in your cluster environment.