cgDist v0.1.0

Archived release of cgDist for scientific publication.

cgDist: Nucleotide-Level Distance Calculation from cgMLST Allelic Profiles

This release corresponds to the implementation described in our manuscript.

Key Features

• SNP and InDel-level distance calculation from cgMLST allelic profiles
• Unified cache architecture for incremental surveillance
• Multi-mode distance calculations (SNPs-only, SNPs+InDel-events, SNPs+InDel-bases)
• Integrated recombination detection

Citation

bioRxiv preprint: https://doi.org/10.1101/2025.10.16.682749

Links

• GitHub repository: https://github.com/genpat-it/cgDist
• Documentation: See README.md

cgDist v0.1.0

Archived release of cgDist for scientific publication.

cgDist: Nucleotide-Level Distance Calculation from cgMLST Allelic Profiles

This release corresponds to the implementation described in our manuscript.

Key Features

• SNP and InDel-level distance calculation from cgMLST allelic profiles
• Unified cache architecture for incremental surveillance
• Multi-mode distance calculations (SNPs-only, SNPs+InDel-events, SNPs+InDel-bases)
• Integrated recombination detection

Citation

bioRxiv preprint: https://doi.org/10.1101/2025.10.16.682749

Links

• GitHub repository: https://github.com/genpat-it/cgDist
• Documentation: See README.md