cgDist

cgDist bridges the resolution gap between traditional cgMLST and SNP-based methods by calculating nucleotide-level pairwise SNP and InDel distances directly from core genome multilocus sequence typing (cgMLST) allelic profiles for efficient bacterial genomic surveillance and outbreak investigation.

Key Features:

• Unified cache architecture: Stores comprehensive alignment statistics to enable multiple distance calculation modes without redundant computation.
• Multiple cache generation modes: Supports both dataset-specific and schema-complete cache generation.
• Streaming analysis capability: Transforms genomic surveillance from batch processing to continuous streaming analysis with cumulative performance benefits as alignment data accumulates.
• Precision zoom lens functionality: Functions as a targeted approach for detailed investigation of clusters identified through initial cgMLST screening without restructuring entire population relationships.
• Distance consistency guarantee: Ensures that cgDist distances are always greater than or equal to corresponding cgMLST distances, preserving epidemiological interpretability while adding genetic discrimination.
• Integrated recombination detection: Leverages cached alignment statistics to identify potential horizontal gene transfer events through mutation density analysis.

Scientific Applications:

• Bacterial genomic surveillance: Enables routine deployment of enhanced-resolution genomic analysis within the computational constraints of public health laboratories.
• Outbreak investigation: Provides nucleotide-level variation critical for source attribution that traditional cgMLST distance calculations may obscure.
• Cluster refinement: Serves as a precision analytical tool for detailed investigation of clusters identified through initial cgMLST screening.
• Recombination detection: Identifies potential horizontal gene transfer events through mutation density analysis of cached alignment statistics.

Methodology:

cgDist calculates nucleotide-level pairwise SNP and InDel distances directly from cgMLST allelic profiles using a unified cache architecture that stores comprehensive alignment statistics.