🦠 AcinetoScope v1.2.0 – "The One Where We Finally Gave Up on PlasmidFinder and Rewrote Half the Universe"
Release date: 2026-05-29
Coffees consumed: > 200
Sane commits: 0
If you’ve ever tried to type plasmids in A. baumannii with PlasmidFinder, you know the pain. It’s like asking a fish to climb a tree. So we did what any sleep‑deprived bioinformatician would do: we built our own damn plasmid typing module. And then we got carried away. This release is huge. No, really. Scroll down.
🧬 1. APT Plasmid Typing – Because Acinetobacter Deserves Better
The Acinetobacter Plasmid Typing (APT) scheme [Lam et al., 2023; Lam & Hamidian, 2024; Tobin et al., 2025] is now fully integrated. No more staring at empty PlasmidFinder outputs.
- Uses
blastnagainst curated rep genes (Rep1, Rep3, RepPriCT). - Thresholds: ≥95% identity, ≥70% subject coverage (as the APT gods intended).
- Spits out per‑genome TSV, per‑genome HTML, and a glorious cross‑genome summary with rep type frequencies and genome‑level lists.
- Validated on 140 public genomes → 100% concordance. You’re welcome.
In the 145‑genome demo: 41 unique rep types, top hits RP‑T1, R3‑T60, R3‑T1. PlasmidFinder? It found 6 replicons, total. We’re not saying it’s useless, but… actually we are.
🎨 2. The Reporter Ate Steroids – Now It's Actually Usable
We took the already‑nice HTML report and gave it the love it deserved. This is what you get when a bioinformatician discovers JavaScript and refuses to sleep.
🔍 Search & Highlight – Finally Everywhere
- Sample Overview, MLST, Capsule, Combinations, Plasmid tabs now have two search boxes:
- Filter rows – hides non‑matching rows.
- Highlight text – turns matches yellow without nuking the HTML structure.
- Genome tags (the little badges) stay put – they just change colour. No more disappearing acts.
🏷️ Genome Tags – No More Comma Hell
Every sample list is now a collection of clickable, highlightable, scrollable tags. Because reading “AC1119, AC1224, AC1532…” is for masochists.
🦠 Virulence Tab – Fixed (Finally)
Virulence genes no longer squat in the AMR tab. They now live where they belong – in the Virulence tab. Took us 2.1 versions, but we got there.
🧬 APT Plasmid Integration
The Plasmids tab now shows:
- APT rep type frequency (Marker, Frequency, Genomes as tags).
- Per‑genome APT rep types (badges, or “No Rep found”).
- Legacy PlasmidFinder results – kept for nostalgia, but clearly marked “legacy”.
📥 Export & Print – One Click
Every table has CSV export. The whole report has a print mode that hides the interactive widgets but keeps your data. Also JSON export for your AI overlords.
🎛️ Filter Buttons Galore
AMR tab: carbapenemases, ESBLs, colistin, tigecycline, etc.
Virulence tab: biofilm, T6SS, iron uptake…
Bacmet tab: biocides, heavy metals, efflux pumps.
We went a little button‑happy. You’re welcome.
🛡️ 3. Error Handling – One Module Dies, Pipeline Keeps Walking
A reviewer once said: “One module should not compromise the total analysis.” We cried a little, then we fixed it.
- Each module runs in a
try/except. If it fails, we log and move on. - Per‑genome failures inside modules don’t kill the whole batch.
- Missing databases? No BLAST? We warn you, but we don’t abort.
Your analysis will finish, even if a single genome tries to ruin your day.
🧹 4. Cleanup – We Now Delete Even More Junk
The orchestrator now cleans up the acineto_plasmid_results directory after copying. No digital litter. No “why is this file still here?”.
🎛️ 5. New CLI Flag
--skip-plasmid – for the rare occasions you want to ignore plasmids. We don’t judge. But we do side‑eye.
🐛 6. Bug Fixes That Will Make You Dance
| Bug | Fix |
|---|---|
| Virulence genes in AMR tab | Fixed – now in Virulence tab. |
| Genome tags vanish after search | Use highlightGenome instead of highlightTableCells. Tags stay. |
| Sample Overview table missing headers | Re‑added <thead>. Sorry. |
| Oxford MLST low assignment rate | Documented as expected (blame draft assemblies). |
| PlasmidFinder gave nothing | Replaced by APT module. Legacy kept for reference. |
| Combination tables comma‑separated mess | Now genome tags. Beautiful. |
| QC table scroll shows white background | Fixed overflow and background colour. |
🌙 7. Late‑Night Realisations (A Short Play)
Week 1: “PlasmidFinder is fine.”
Week 2: “Wait, it’s not finding anything.”
Week 3: “Let’s implement the APT scheme.”
Week 4: “BLAST output parsing is making me question my life choices.”
Week 5: “Why do genome tags disappear? Oh, because we’re replacing the whole cell HTML.”
Week 6: “Let’s rewrite the reporter. Again.”
Week 7: “It works. It finally works.”
Coffee count: 200+. Sane commits: 0.
🙏 8. Acknowledgements – The Giants We Stood On (And Sometimes Borrowed Coffee From)
We are deeply indebted to the open‑source community. Without you, this release would be a pile of broken subprocess calls and regret.
Tools & databases – MLST, Kaptive, AMRFinderPlus, ABRicate, Biopython, psutil, BLAST+, CARD, ResFinder, ARG‑ANNOT, MEGARes, VFDB, Ecoli_VF, PlasmidFinder (yes, even you), EcoH, BacMet2. You are the real MVPs.
APT scheme & maintainers – Margaret M.C. Lam, Jonathan Koong, Kathryn E. Holt, Ruth M. Hall, Mehrad Hamidian, Liam A. Tobin. You gave us a proper rep typing scheme. We owe you many beers.
Validation dataset – Din et al. (Microbial Genomics, 2025). Without your 126 A. baumannii isolates, our validation would have been a lot shorter (and more embarrassing).
Python, Conda, GitHub – for keeping us (mostly) sane.
To my co‑authors and the caffeine industry – I owe you my sanity.
If we forgot you, open an issue. We’ll add you. It’s the sleep deprivation.
⭐ 9. Show Some Love
If AcinetoScope made your A. baumannii analysis less painful, star the repo and share it with your fellow outbreak investigators.
Now go forth, type acinetoscope -i "*.fna" -o results/, and may your contigs be long and your plasmids be typed.
🦠🧬💻
P.S. If you find a bug, please report it. But be gentle – my sleep cycle is still recovering.