EnteroScope is a complete, automated genomic analysis pipeline for Enterobacter cloacae complex, 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) – Enterobacter cloacae specific scheme • Antimicrobial Resistance (AMR) – Resistance gene detection via AMRfinderPlus • Virulence & Plasmid Profiling (ABRicate) – Multi-database screening (CARD, ResFinder, VFDB, NCBI, MEGARes, BacMet, PlasmidFinder) • Critical Genes Flagging – Priority markers for infection control (carbapenemases, ESBLs, colistin, tigecycline) • Interactive HTML Reports – Gene-centric integrated analysis • Cross-genome pattern discovery

Key Features: 🚀 Parallel Execution – QC and MLST run simultaneously for maximum speed 📊 Interactive Reports – HTML summaries with search, sort, export, print 🧬 Multi-Database Integration – AMRfinderPlus + ABRicate with 10+ databases ⚡ Easy Deployment – Single command analysis with automatic result aggregation 🎯 Critical Gene Tracking – Carbapenemases (KPC, NDM, OXA-48), ESBLs, mcr, tet(X), biofilm, efflux pumps

Designed for clinical microbiology, outbreak investigation, and genomic surveillance, EnteroScope provides clinical labs and researchers with a complete solution for Enterobacter cloacae complex genomic characterization from raw sequencing data to publication-ready reports.