QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.


Category:  Bioinformatics


Usage Notes

QIIME:
To show the software versions: module avail qiime

 

Loading the module will set the path and any necessary variables:  module load qiime/version


Note: Pre-requisite modules (e.g. R and python/anaconda) must be loaded first



QIIME2:

To show the software versions: module avail qiime2


Loading the module will set the path and any necessary variables:  module load qiime2/version


Examples for running QIIME2 can be found on the cluster under:

/util/common/qiime2/example-atacama    (parallel example)


/util/common/qiime2/example-moving-pictures (serial example)

 



Additional Information


Guidance on running QIIME on the cluster is provided in the .pdf file given below.