hicap

hicap predicts serotype and identifies the structure of the capsule biosynthesis locus (cap locus) from Haemophilus influenzae genome assemblies.

Key Features:

• In silico serotyping: Rapidly predicts the six known H. influenzae capsule serotypes (a to f), each encoded by distinct variations of the cap locus (cap-a to cap-f).
• Cap locus identification: Identifies cap loci in genome assemblies and determines their structural configuration.
• Hybrid locus detection: Identifies hybrid cap loci arising from recombination between lineages.

Scientific Applications:

• Genomic epidemiology: Tracks the distribution and diversity of encapsulated H. influenzae strains in genomic surveillance studies.
• Vaccine impact monitoring: Assesses serotype prevalence in post-vaccine era populations and in countries without vaccination programs.
• Virulence association studies: Investigates the relationship between polysaccharide capsule serotype and invasive disease potential.

Methodology:

hicap is written in Python3 and analyzes H. influenzae genome sequences to predict cap locus serotype and structure.