Scoary

Scoary performs pan-genome wide association studies by testing associations between accessory genes and phenotypic traits across bacterial genomes.

Key Features:

• Input Compatibility: Accepts a gene_presence_absence.csv file produced by Roary and a user-created traits file linking genomes to phenotypic traits.
• Association Analysis: Calculates associations between all accessory genes (genes present in more than one but fewer than all genomes) and specified traits.
• Sorting by Association Strength: Outputs lists of genes ranked by the strength of their association with each trait.
• Population Stratification: Accounts for population stratification to reduce confounding from underlying population structure.
• Minimal Assumptions: Operates with minimal assumptions about evolutionary processes across bacterial species.

Scientific Applications:

• Pan-genome wide association studies: Identify gene-trait associations within bacterial accessory genomes.
• Microbial genetics: Map accessory genes linked to specific bacterial phenotypes.
• Evolutionary biology: Investigate genetic contributions to phenotypic diversity and adaptation in bacterial populations.
• Applied microbiology: Support studies that relate accessory gene content to phenotypic outcomes in applied microbiology contexts.

Methodology:

Uses Roary's gene_presence_absence.csv and a traits file to test associations between accessory genes (present in >1 and <all genomes) and traits, outputs genes ranked by association strength, and accounts for population stratification while operating with minimal evolutionary assumptions.