Merge pull request #642 from TheJacksonLaboratory/update-readme

Update README

README.md

@@ -1,29 +1,40 @@
+# LIRICAL
+
 [![GitHub release](https://img.shields.io/github/release/TheJacksonLaboratory/LIRICAL.svg)](https://github.com/TheJacksonLaboratory/LIRICAL/releases)
 [![Java CI with Maven](https://github.com/TheJacksonLaboratory/LIRICAL/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/TheJacksonLaboratory/LIRICAL/actions/workflows/maven.yml)
 
-# LIRICAL
 LIRICAL (LIkelihood Ratio Interpretation of Clinical AbnormaLities) 
 is designed to provide clinically interpretable computational analysis of phenotypic
 abnormalities (encoded using the [Human Phenotype Ontology](http://www.human-phenotype-ontology.org)),
 optionally combined with an analysis of variants and genotypes if a VCF file is provided with the
 results of diagnostic gene panel, exome, or genome sequencing.
 
-A manuscript describing LIRICAL is available at the 
-[American Journal of Human Genetics](https://pubmed.ncbi.nlm.nih.gov/32755546/).
+The prioritized diseases are reported in human-friendly HTML report. 
+The report summarizes the most likely differential diagnoses:
+
+<img src="docs/_static/lirical-sparkline-lds2.top5.png" alt="Top matches" width="800"/>
+
+and breaks down the contributions of the HPO terms and deleterious variants in the associated genes for each diagnosis:
+
+<img src="docs/_static/lirical-detailed-TGFBR2.png" alt="" width="800" title="Diff dg"/>
+
+The report is also available in JSON/TSV formats suitable for programmatic post-processing.
 
 
 ## Availability
-Most users should download the latest distribution ZIP file from
-the [Releases page](https://github.com/TheJacksonLaboratory/LIRICAL/releases).
 
+Most users should download the latest distribution ZIP file from the [Releases page](https://github.com/TheJacksonLaboratory/LIRICAL/releases).
+
+
+## Learn more
 
-## Documentation
-Please consult the documentation for installation instructions and a tutorial:
-- [reference documentation](https://thejacksonlaboratory.github.io/LIRICAL/stable)
-- [edge release documentation](https://thejacksonlaboratory.github.io/LIRICAL/latest)
+Read more about the LIRICAL *algorithm* 
+in the manuscript available at the [American Journal of Human Genetics](https://pubmed.ncbi.nlm.nih.gov/32755546/).
 
+Consult the documentation for *installation instructions* and a *tutorial*:
+- [Stable documentation](https://thejacksonlaboratory.github.io/LIRICAL/stable)
+- [Edge release documentation](https://thejacksonlaboratory.github.io/LIRICAL/latest)
 
-## API docs
-Developers can access Javadoc at:
-- [reference](https://thejacksonlaboratory.github.io/LIRICAL/stable/apidocs)
-- [edge release](https://thejacksonlaboratory.github.io/LIRICAL/latest/apidocs)
+Developers can access *API reference* at:
+- [Stable](https://thejacksonlaboratory.github.io/LIRICAL/stable/apidocs)
+- [Edge release](https://thejacksonlaboratory.github.io/LIRICAL/latest/apidocs)