AcinetoScope is a complete, automated genomic analysis pipeline for Acinetobacter baumannii, 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) - Oxford & Pasteur schemes • K/O Locus Typing (Kaptive) - Capsule and lipooligosaccharide typing • Antimicrobial Resistance (AMR) - Comprehensive resistance gene detection • 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

Key Features: 🚀 Parallel Execution - All modules run simultaneously for maximum speed 📊 Interactive Reports - HTML summaries with visualization 🧬 Multi-Database Integration - CARD, ResFinder, VFDB, NCBI, MEGARes, BacMet ⚡ Easy Deployment - Single command analysis with automatic dependency handling 🎯 Critical Gene Tracking - Carbapenemases, ESBLs, colistin/tigecycline resistance

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

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