BacTaxID: reproducible analysis pipeline and genomic datasets for publication

BacTaxID Supplementary Analysis Workflow Description This repository contains the complete reproducible analytical workflow for validating and benchmarking the BacTaxID bacterial typing system. The analysis encompasses comprehensive performance evaluation across multiple clinically relevant bacterial genera, including comparative studies with established typing methodologies and outbreak detection case studies. Overview BacTaxID is a hierarchical k-mer-based bacterial classification system that assigns genomic signatures to six similarity levels (L_0 through L_5) k-mer profiling algorithms and pseudo-clique clustering approach. This supplementary material provides detailed computational analysis for BacTaxID classifications and comparissons with: cgMLST Multi-locus sequence typing (MLST) In silico serotyping (HiCap, SISTR, ClermonTyping) Phylogenetic grouping systems Species-level profiling tools (Sylph, miniphy) Alternative ANI estimation methods (Mash, Sourmash, BinDash) Analysis Scope 1. Database Completeness Assessment Quantification of classification completeness across hierarchical levels Correlation analysis between database size and classification success Distribution of reference genomes across bacterial genera Identification of sampling biases and coverage gaps 2. Genus Validation Acinetobacter Campylobacter Clostridioides Enterobacter Enterococcus Haemophilus Klebsiella Listeria Mycobacterium Neisseria Pseudomonas Staphylococcus Streptococcus Vibrio