Difference between revisions of "QIIME2"
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|qiime2}} | |{{#vardefine:app|qiime2}} | ||
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| − | == | + | ==Environment Modules== |
| − | < | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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 | 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 | echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc | ||
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|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 15:15, 19 August 2022
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.
Environment Modules
Run module spider qiime2 to find out what environment modules are available for this application.
System Variables
- HPC_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