update readme

README.md

@@ -1,5 +1,23 @@
 # katharoseq
+![](https://github.com/qiime2/q2templates/workflows/ci/badge.svg)
+
+Katharoseq is a qiime2 plugin for analyzing samples with low biomass.
 
 ## Installation
-pip install -e .
+To install, download this repository and navigate to the `q2_katharoseq` folder and run:
+    pip install -e .
+
+## Usage
+
+    qiime katharoseq read-count-threshold \
+        --p-threshold 50 \
+        --i-table table.qza \
+        --m-positive-control-column-column p_control \
+        --m-positive-control-column-file metadata.tsv \
+        --p-positive-control-value katharoseq_control \
+        --p-control classic \
+        --m-cell-count-column-column max_cell_count \
+        --m-cell-count-column-file metadata.tsv \
+        --o-visualization visualization.qzv \
+