Detailed README

README.md

@@ -1,6 +1,22 @@
-AB_SA
+AB_SA - Source attribution based on accessory genes
 ========
+Predicts the source of bacterial strains based on their accessory genes.
+
+## Contents
+  * [Introduction](#introduction)
+  * [Input data](#input-data)
+    * [Pangenome](#pangenome)
+    * [Genes enriched](#genes-enriched)
+
+## Introduction
 
 The AB_SA ("Accessory-based source attribution") method aims at attributing the origin of bacterial strains associated to human cases or isolated in environment. 
-AB_SA method relies on accessory genes and multinomial logistic model. AB_SA uses as input a list of enriched genes in the sources, it trains and tests the multinomial logistic model and can predict  genomes of strains with unknown sources  
+AB_SA method relies on accessory genes and multinomial logistic model. AB_SA uses as input a list of enriched genes in the sources, it trains and tests the multinomial logistic model and can predict  genomes of strains with unknown sources.  
+
+
+## Input data
+
+### Pangenome
+The pangenome of the strains (both strains from the sources and the strains to attribute) included in the study should be determined. The AB_SA method parses the Rtab produced by [Roary] (http://sanger-pathogens.github.io/Roary) 
 
+### Genes enriched