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support:hpc:software:qiime

Qiime

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.

To load Qiime type the following:

$ module load gcc R openmpi python perl qiime 

Running

Here is an example submit script that will run the entire verification suite (some 2000+ unit tests).

First make a copy of the test directory

$ module load gcc R openmpi python perl qiime 
$ cp -rp $QIIME_HOME/tests .
$ cd tests
$ vi q.sh

Then in q.sh:

#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#$ -pe threaded 4

hostname
module load gcc R openmpi python perl qiime
python all_tests.py 

To run the tests (this takes some 10s of minutes):

$ qsub q.sh

The Qiime Tutorial also works, you just have to run the module load command first.

support/hpc/software/qiime.txt · Last modified: 2013/01/08 17:34 by bill