update to readme

README.md

@@ -1,5 +1,34 @@
-# katharoseq
+# KatharoSeq
+
+An implementation of the KatharoSeq protocol, originally defined in [Minich et al 2018 mSystems](https://journals.asm.org/doi/10.1128/mSystems.00218-17).
 
 ## Installation
+
+Installation assumes a working QIIME 2 environment with a minimum version of 2021.8. Details on installing QIIME 2 can be found [here](https://docs.qiime2.org/2021.11/install/).
+
+```
+git clone https://github.com/biocore/q2-katharoseq.git
+cd q2-katharoseq
 pip install -e .
-
+``` 
+
+## Use
+
+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`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy
+classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) 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
+```