An implementation of the KatharoSeq protocol, originally defined in Minich et al 2018 mSystems.
Installation assumes a working QIIME 2 environment with a minimum version of 2021.8. Details on installing QIIME 2 can be found here.
git clone https://github.com/biocore/q2-katharoseq.git
cd q2-katharoseq
pip install -e .
Computation of a minimum read count threshold can be performed with the
read_count_threshold plugin action. Computation assumes that the user has
classified their 16S features against SILVA, and that the
FeatureTable[Frequency] has been collapsed to the genus level. Please see the
q2-feature-classifier for detail on how to perform taxonomy
classification, and the q2-taxa plugin for information on collapsing to a taxonomic level.
qiime katharoseq read_count_threshold \
--i-table a_genus_level_table.qza \
--p-control classic \
--p-positive-control-value name_of_controls_in_metadata \
--m-positive-control-column-file your_metadata.tsv \
--m-positive-control-column-column sample_type_variable_in_metadata \
--m-cell-count-column-file your_metadata.tsv \
--m-cell-count-column-column cell_count_variable_in_metadata \
--o-visualization result.qzv