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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.

How to Use

Warning: QIIME is a complex pipelining application. It is not fully tested on Helix Systems. There may be some features that are not implemented yet, so please report any anomalous or missing behavior to

Note: We now have a license for the 64-bit version of usearch. To run methods with this version, include

-m usearch7.0

in your QIIME commands instead of -m usearch61.

Create a qsub script like this example (

#PBS -N qiimeRun
#PBS -o qiimeRun.o
#PBS -e qiimeRun.e


# Load qiime module
module load qiime

# Pre-processing
rm -rf mapping_output ; -m Fasting_Map.txt -o mapping_output -v
rm -rf split_library_output ; -m Fasting_Map.txt -f Fasting_Example.fna -q Fasting_Example.qual -o split_library_output
rm -rf otus ; -i split_library_output/seqs.fna -o otus -a -O 16

#OTU Heatmap -i otus/otu_table.biom -o otus/OTU_Heatmap/

#OTU Network -m Fasting_Map.txt -i otus/otu_table.biom -o otus/OTU_Network

# etc, etc, etc ...

Parallel processing can be controlled by including the -a -O cpu switches to the QIIME scripts. See the QIIME documentation for more information. The above example can be submitted to a c16 node:

qsub -l nodes=1:c16

The default configuration for QIIME is set via the file $QIIME_HOME/qiime_config. You may override these defaults by creating your own version of this file in your /home directory:

cp $QIIME_HOME/qiime_config ~/.qiime_config

and then edit the ~/.qiime_config file to your liking before running your QIIME scripts.

Standard Reference Files

Once the QIIME module is loaded and your environment is set, then standard reference files can be found in:

ls $QIIME_HOME/../seq

These include Silva, OTUS, and UNITE files.

Visualizing Results

Some of the output files will be html format. These can be visualized most easily by mounting your /home or /data areas on your desktop machine, and then opening them with a web browser of your choice. Other file formats may require third-party applications for display.

Phylogenetic files of tre format can be displayed with FigTree. If you have an X-windows connection to Helix, you can display these using the system-installed FigTree application like so:

figtree [file].tre