chewBBaca

chewBBACA performs gene-by-gene schema creation and allele calling for core genome and whole-genome MultiLocus Sequence Typing (cg/wgMLST) to support bacterial genomic epidemiology and outbreak detection.

Key Features:

• Schema Creation and Evaluation: Creates and evaluates typing schemas focused on core genome or whole-genome loci for cg/wgMLST analyses.
• Allele Calling: Performs allele calling on complete or draft genomes, identifying allelic variants corresponding to defined schemas.
• Assembly Compatibility: Accepts input from de novo assemblers and processes assembled genomes for allele identification.
• Execution Environments: Supports execution on single workstations and high-performance computing clusters.
• Implementation: Implemented in Python 3.4 or higher.

Scientific Applications:

• Bacterial Genomic Epidemiology: Enables gene-by-gene analyses to characterize bacterial isolates for epidemiological investigations.
• Outbreak Detection and Investigation: Provides high-resolution cg/wgMLST-based allele profiles to identify and delineate outbreak clusters.
• Population Structure and Evolution: Facilitates examination of bacterial population structures and evolutionary relationships using allele-based schemas.

Methodology:

Users define typing schemas from genomic data (core genome or whole-genome), and the software processes assembled genomic sequences to call alleles corresponding to the defined schema, operating on complete or draft assemblies including outputs from de novo assemblers.