CamPype

CamPype performs automated analysis of bacterial whole-genome sequencing (WGS) data to process reads, assemble genomes, and identify typing, antibiotic resistance, virulence genes, plasmids, pangenomes, and nucleotide variants with a focus on Campylobacter species.

Key Features:

• Customizable workflow: Configurable analysis stages and tool selection to accommodate different processing needs for bacterial WGS data.
• Read quality control filtering: Filters sequencing reads to ensure high-quality input for downstream analyses.
• Contamination detection: Identifies and removes contaminant sequences from datasets.
• Read extension and assembly: Extends reads and assembles them into draft genomes.
• Bacterial typing: Determines strain identification and classification from genomic data.
• Genome annotation: Identifies and annotates genomic features within assembled genomes.
• Antibiotic resistance and virulence gene detection: Detects genes associated with antibiotic resistance and virulence factors.
• Plasmid identification: Identifies plasmid sequences present in genomic assemblies.
• Pangenome construction: Builds pangenomes to assess gene presence–absence across strains.
• Nucleotide variant identification: Calls nucleotide-level variants among genomes.
• Interactive HTML reporting: Compiles analysis results into an interactive HTML report.

Scientific Applications:

• Clinical microbiology: Bacterial typing and characterization from WGS for clinical isolates.
• Food microbiology: Genomic analyses for pathogen detection and characterization in food-related investigations.
• Epidemiological surveillance: Strain tracking and outbreak analysis using typing, variant, and pangenome data.
• Campylobacter research: Genomic studies focused on Campylobacter species, including resistance and virulence profiling.

Methodology:

Computational steps explicitly include read quality control filtering, contamination detection, read extension and assembly, bacterial typing, genome annotation, antibiotic resistance and virulence gene detection, plasmid identification, pangenome construction, nucleotide variant identification, and generation of an interactive HTML report.