Welcome to PathoFact's wiki!

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.

Overview

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.

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

• Installation: Requirements and Dependencies

• Input

• Usage

• Test module

• Reporting