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 classification 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 taxonomic levels (L_0 through L_5) using locality-sensitive hashing (LSH) and k-mer profiling algorithms. This supplementary material provides detailed computational validation demonstrating that BacTaxID classifications exhibit strong concordance with: 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. Taxonomic Concordance Validation Eight clinically important bacterial genera analyzed: Klebsiella species complex - Validation against Kleborate (MLST, virulence, resistance) Haemophilus species complex - HiCap capsular serotyping and MLST concordance Salmonella enterica - Serovar prediction, cgMLST, and SISTR concordance Escherichia coli - Phylogroup assignment (ClermonTyping) and MLST validation Streptococcus species - MLST-based typing concordance Staphylococcus species - Species identification and ST distribution Enterococcus species - Species-level resoluti