Difference between revisions of "QIIME2"

Revision as of 14:43, 8 December 2017

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.

Required Modules

System Variables

HPC_{{#uppercase:qiime2}}_DIR - installation directory

Additional Information

If you encounter an 'Invalid DISPLAY variable' error using some qiime2 tools like 'qiime demux summarize' set the default matplotlib backend to Agg in your personal configuration with

echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc

Citation

If you publish research that uses qiime2 you have to cite it as follows:

J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303

@@ Line 44: / Line 44: @@
 If you encounter an 'Invalid DISPLAY variable' error using some qiime2 tools like 'qiime demux summarize' set the default matplotlib backend to Agg in your personal configuration with
   echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
-If you get an 'out of space' error in your job log try using the <code>TMP</code> variable instead of relying on the <code>TMPDIR</code> automatically set by SLURM. QIIME2 appears to have a problem with temporary directory locations. E.g. add the following to your job script before you call qiime2:
- export TMP=${TMPDIR}
 |}}
 <!--Job Scripts-->