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Commit d95ad763 authored by Laura Denies's avatar Laura Denies
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parent 70401ab2
# PathoFact 1.1
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.
# Requirements
PathoFact requires a good working Python (3.6.4), snakemake (version 5.5.4) and (mini)conda installation.
If snakemake is not yet installed one could install this by using the provided conda file (snakemake.yaml)
To install run: conda env create -f snakemake.yaml
PathoFact provides the
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