q2-coremicrobiome

Qiime2 plugin of COREMIC: CORE MICrobiome [https://doi.org/10.7717/peerj.4395]. This plugin works with qza files from QIIME 2.

• For Biom v1 OTU tables from QIIME 1.x, please use the web-tool: http://coremic2.appspot.com/

Install from conda:

conda install -c richrr q2-coremicrobiome

Sample usage:

qiime coremicrobiome full-pipeline --help

qiime coremicrobiome full-pipeline --i-table /path/to/otu_table_file/table.qza --p-factor Person --p-group Good --p-outputfile coremic.q2 --m-groupfile-file /path/to/meta_data_file/sampleSheet.txt --p-make-relative --o-visualization output.qzv

Please note:

• SampleSheet (map file) should have "SampleID" as the header for first column. Any other string or its variation (e.g. "#SampleID", "SAMPLEID") will NOT work.
• creates "output.qzv" in current directory.

Sample data available at:

https://github.com/richrr/sample_data/tree/master/q2-coremicrobiome

To get sample data and test the qiime plugin, in Unix or Mac terminal:

mkdir dataset1

cd dataset1

wget https://raw.githubusercontent.com/richrr/sample_data/master/q2-coremicrobiome/dataset1/map-file.txt

wget -O table.w.taxaname.qza https://github.com/richrr/sample_data/blob/master/q2-coremicrobiome/dataset1/table.w.taxaname.qza?raw=true

qiime coremicrobiome full-pipeline --i-table table.w.taxaname.qza --p-factor Plant --p-group Sw --p-outputfile coremic.q2 --m-groupfile-file map-file.txt --p-make-relative --o-visualization swg.qzv

OR

mkdir dataset2

cd dataset2

wget https://raw.githubusercontent.com/richrr/sample_data/master/q2-coremicrobiome/dataset2/map-file.txt

wget -O table.qza https://github.com/richrr/sample_data/blob/master/q2-coremicrobiome/dataset2/table.qza?raw=true

qiime coremicrobiome full-pipeline --i-table table.qza --p-factor SampleType --p-group Leaf --p-outputfile out.Leaf. --m-groupfile-file map-file.txt --p-make-relative --p-quantile-normalize --o-visualization output.Leaf.qzv