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 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. If you need more information on how to process your data, please refer to one of the relevant tutorials that can be found here.
Computation of a minimum read count threshold can be performed with the
read_count_threshold plugin action. Test data can be found under the testdata folder.
qiime katharoseq read_count_threshold \
--i-table example/example_table_genus.qza \ # a genus level table
--p-threshold 80 \
--p-control classic \
--p-positive-control-value katharoseq_control \ # name of controls in metadata
--m-positive-control-column-file example/simple_katharoseq_metadata.tsv \ # your metadata
--m-positive-control-column-column control_or_sample \ # sample type variable in metadata
--m-cell-count-column-file example/simple_katharoseq_metadata.tsv \
--m-cell-count-column-column max_cell_count \ # cell count variable in metadata
--o-visualization result.qzv
qiime katharoseq read_count_threshold
--i-table example.qza \ # a_genus_level_table
--p-threshold 80
--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