Description
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 staff@helix.nih.gov
QIIME is a collection of a multitude of scripts and executables. You will need to set your environment using the command
module load qiimeYou could run the scripts directly from the commandline, but it is generally easier to create a script. A good place to start is by running the tutorial.
unzip $QIIME_HOME/src/qiime_tutorial-v1.5.0.zip cd qiime_tutorial-v1.5.0 ./qiime_tutorial_commands_serial.shHave a look at the qiime_tutorial_commands_serial.sh script to see what is being done.
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_configand then edit the ~/.qiime_config file to your liking before running your QIIME scripts.
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
