microGWAS

microGWAS performs large-scale bacterial genome-wide association studies by integrating multiple software tools into a reproducible workflow for identifying genetic variants associated with bacterial phenotypes.

Key Features:

• Multiple Variant Types: The pipeline runs associations using five sets of genetic variants: unitigs, gene presence/absence, rare variants (gene burden test), gene cluster specific k-mers, and all unitigs jointly.
• Functional Annotation: All variants passing the association threshold are annotated to identify overrepresented biological processes and pathways.
• Phylogenetic Analysis: Results can be augmented by generating a phylogenetic tree.
• Resistance and Virulence Prediction: The pipeline predicts the presence of antimicrobial resistance and virulence associated genes.
• Multi-phenotype Support: The pipeline accepts multiple phenotypes as targets for association testing.

Scientific Applications:

• Virulence Association Mapping: The pipeline identifies genetic variants associated with bacterial virulence, as demonstrated on an E. coli dataset.
• Antimicrobial Resistance Research: The pipeline predicts and analyzes antimicrobial resistance associated genes.
• Host Preference Studies: Genetic variants associated with bacterial host preference can be identified.
• Bacterial Trait Mechanism Elucidation: The pipeline enables better understanding of mechanisms involved in bacterial phenotypes such as virulence, host preference, and antimicrobial resistance.

Methodology:

The pipeline accepts a set of assemblies and annotations as input, runs associations using five variant sets, annotates significant variants for biological processes and pathways, generates a phylogenetic tree, and predicts antimicrobial resistance and virulence associated genes.