Klebogenomics Code Scripts

This repository contains the full, reproducible workflow for a secondary genomic analysis of a neonatal Klebsiella pneumoniae sepsis outbreak in Zambia using public ENA whole-genome sequencing data. The pipeline assembles and QC-filters genomes, confirms species and sequence types, profiles antimicrobial resistance and virulence (including Kleborate resistance/virulence scores), characterises plasmids using MOB-suite (replicon typing, mobility prediction, and plasmid clustering), and evaluates plasmid relatedness using replicon-content clustering (Jaccard distance; dendrogram + heatmap) plus Mash distance-based similarity summaries within MOB-suite plasmid clusters (e.g., AB060). Prophages are detected and annotated using geNomad with MMseqs2 support. Outputs include manuscript-ready tables/figures and an Access Microbiology–compliant open-data package (MANIFEST, versions, scripts, and supplementary legends).