Difference between revisions of "QIIME2"

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[[Category:Software]][[Category:Biology]][[Category:Ecology]]
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[[Category:Software]][[Category:Biology]][[Category:genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|qiime2}}
 
|{{#vardefine:app|qiime2}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
<!--
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* 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
 
 
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-->
 
<!--Job Scripts-->

Latest revision as of 15:15, 19 August 2022

Description

qiime2 website  

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