Kleboscope is a complete, automated genomic analysis pipeline for Klebsiella pneumoniae, featuring parallel execution for rapid processing of bacterial genomes. The pipeline integrates multiple analysis modules into a unified workflow:

• Quality Control (FASTA QC) – Comprehensive sequence validation • Multi‑Locus Sequence Typing (MLST) – Pasteur scheme • K/O Locus Typing (Kaptive) – Capsule and lipopolysaccharide typing • Antimicrobial Resistance (AMR) – AMRfinderPlus and ABRicate databases • Virulence & Plasmid Profiling (ABRicate) – Multi‑database screening • Critical Genes Flagging – Priority markers for infection control • Interactive HTML Reports – Gene‑centric integrated analysis • Cross‑genome pattern discovery

Critical Genes Tracked: 🔴 Carbapenemases (KPC, NDM, OXA‑48) 🟠 Colistin (mcr) 🟡 Tigecycline (tetX) 🟢 ICEKp Markers (ybt, clb, iro, rmp) 🔵 Virulence Plasmid Markers (iro, iuc, rmp, rmpA2) 🟣 Biocides & Heavy Metals (qac, sil, mer, ars, pco) ⚪ Adhesins (fim, mrk, ecp) 🔶 Secretion Systems (tss) 💧 Siderophores 🧪 Toxins

Key Features: 🚀 Parallel Execution – Independent modules run concurrently for maximum speed 📊 Interactive Reports – HTML summaries with visualisation 🧬 Multi‑Database Integration – CARD, ResFinder, VFDB, NCBI, MEGARes, BacMet, etc. ⚡ Easy Deployment – Single command analysis with automatic dependency handling 🎯 Comprehensive Gene Tracking – Resistance, virulence, plasmid, and environmental markers

Designed for clinical microbiology, outbreak investigation, and genomic surveillance, Kleboscope provides clinical labs and researchers with a complete solution for K. pneumoniae genomic characterisation from raw sequencing data to publication‑ready reports.

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