StaphScope: A species-optimized computational pipeline for rapid and accessible Staphylococcus aureus genotyping and surveillance

STAPHSCOPE VERSION 1.2.0 🚀 Major Improvements 🔬 Ultimate Reporter (Massive Upgrade) FASTA QC tab – View all assembly metrics (N50, GC%, total length, etc.) in a sortable table. AI Assistant Guide – Example prompts to use with ChatGPT/Claude/Gemini. Let AI do the talking. 20 filter buttons each for AMR & Virulence tabs – One‑click filters for mecA, PVL, TSST‑1, enterotoxins, and more. Combination tables – ST‑spa, ST‑SCCmec, spa‑SCCmec under MLST, spa, SCCmec, and MRSA tabs (searchable, sortable, no truncation). Sortable headers – Click any column header to sort ascending/descending. Info boxes – Detailed explanations of gene families (e.g., "Role of each AMR gene family in S. aureus"). No truncation – Genome lists are complete. Scroll horizontally if needed. 🧬 AMR Module (Dynamic Database) Dynamic database detection – Finds the latest 20* folder in data/amrfinder_db/. No more hardcoded 2026-03-24.1. --update-db flag – Downloads the latest AMRfinderPlus database (no PhD required). --db-version flag – Shows current database version. Graceful failure – Orchestrator skips AMR if database missing, instead of crashing. 🛡️ SCCmec Module sccmec_database.sh – Clones the latest SCCmec database from Bitbucket into database/. One script to rule them all. 🧬 MLST Module mlst_database.sh – Downloads the MLST database (kept in Git, but script ensures latest). 🐳 Dockerfile Containerised – Automatic abricate --setupdb and AMR database download during build. User goes straight to analysis! 🎛️ Orchestrator Version 1.2.0 – Skips AMR analysis if database missing (no more tantrums). --update-amr-db flag – Update AMR database from the orchestrator directly. 🐛 Bug Fixes Fixed a rename error where __init__.py was turned into a binary test file. Git got confused; we apologised. Removed hardcoded database versions – the future is dynamic. 📦 What's still missing? (User responsibilities) Conda users must run staphscope --help for mandatory commands prior analysis Docker/Singularity users just go strait.......... 🎉 Humble brag This release adds ~80 files, 228k insertions, and removes 1k lines of hardcoded misery. Ultimate Reporter now has more tables than a database conference and filter buttons for days. StaphScope is now more flexible than a yoga instructor and smarter than your average pipeline. Enjoy, and may your sequencing runs be ever in your favour.