ichewieSnake

ichewieSnake implements a core genome multilocus sequence typing (cgMLST) workflow for whole-genome sequencing (WGS)-based outbreak investigation and surveillance of bacterial pathogens.

Key Features:

• End-to-end cgMLST pipeline: Provides a cgMLST-based analysis pipeline that accepts assemblies and reads as inputs.
• Integration with chewBBACA: Performs allele calling using chewBBACA and incorporates allele hashing to encode allele profiles.
• Allele hashing and profile comparison: Uses hashed allele profiles to enable comparison of profiles generated in different laboratories without a central nomenclature system.
• Automated analytical steps: Automates computation of allele distance matrices, determination of cluster membership, and phylogenetic reconstruction.
• Cross-laboratory cluster nomenclature: Produces a stable, intercommunicable cluster nomenclature to support joint analyses of allele profiles across laboratories.
• Taxonomic applicability: Applicable to any bacterial taxa with an available cgMLST scheme and demonstrated on Salmonella enterica data.

Scientific Applications:

• Outbreak investigation: Enables WGS-based cgMLST analyses to identify and delineate clusters during bacterial pathogen outbreaks.
• Routine surveillance: Supports routine surveillance of bacterial pathogens through standardized cgMLST profiling and distance-based analyses.
• Cross-laboratory investigations: Facilitates joint outbreak investigations by allowing joining and comparison of allele profiles from multiple laboratories.

Methodology:

Allele calling with chewBBACA, allele hashing of profiles, computation of allele distance matrices, determination of cluster membership, and phylogenetic reconstruction using cgMLST schemes; accepts assemblies and reads as input and was demonstrated on Salmonella enterica data.