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 # Welcome to PathoFact's wiki!
 
-PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance. Additionally, PathoFact combines the prediction of these pathogenic factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the localization of the genes on mobile genetic elements (MGEs), as well as on the chromosome. Furthermore, each module (toxins, virulence factors, and antimicrobial resistance) of PathoFact is also a standalone component, making it a flexible and versatile tool.
+PathoFact is an easy-to-use, modular and reproducible pipeline for the identification of **virulence factors**, **bacterial toxins** and **antimicrobial resistance genes** in metagenomic data.
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+# Overview
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+Pathogenic microorganisms cause disease by invading, colonizing and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. 
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+PathoFact combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact’s modules for virulence factors, toxins and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool.
 
 # Contents
 - [Requirements, Dependencies and Installation](./Requirements and installation)
 - [Input](./Input)
 - [Run Pathofact](./Run PathoFact)
 
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