--- a
+++ b/docs/index.md
@@ -0,0 +1,70 @@
+
+```{include} ../README.md
+```
+
+
+```{toctree}
+:caption: Getting started
+:name: getting_started
+:hidden:
+:maxdepth: 2
+
+getting_started/installation
+getting_started/docker
+getting_started/singularity
+getting_started/vagrant
+```
+
+
+
+```{toctree}
+:caption: Usage Notes
+:name: usage
+:hidden:
+:maxdepth: 2
+
+
+usage/cli
+usage/useful_options
+usage/specializedScans
+usage/templates.md
+usage/faq.md
+```
+
+
+```{toctree}
+:caption: Processing pipeline details
+:name: pipeline_details
+:hidden:
+:maxdepth: 2
+
+pipeline/pipeline
+pipeline/algorithms
+```
+
+
+
+```{toctree}
+:caption: Outputs of HippUnfold
+:name: outputs
+:hidden:
+:maxdepth: 2
+
+outputs/output_files
+outputs/visualization
+outputs/QC
+```
+
+
+
+```{toctree}
+:caption: Contributing
+:name: contributing
+:hidden:
+:maxdepth: 2
+
+contributing/references
+contributing/contributing
+```
+
+