Unified sequence exploration, restriction enzyme analysis, cleavage design, assembly simulation, library prediction, fragment analysis, and Sanger verification platform for the Athey Lab.
Replaces and consolidates functionality from fragment-viewer, golden-gate/registry/,
and seq-registry into a single local platform.
pip install -e ".[dev]"
cd frontend && npm install && npm run build && cd ..
cutscope serveOpen http://localhost:7890 (hotkey: Ctrl+Alt+C)
| Tab | Description |
|---|---|
| Explorer | Browse and search all lab sequences, primers, constructs, gRNAs |
| CutMap | Interactive restriction enzyme site analysis (35+ enzymes, Type IIS) |
| Cleavage | Cas9 PAM scanning, cut prediction, gRNA design + scoring |
| Assembly | Golden Gate simulation: overhang fidelity, validation, assembly chain |
| Library | Model final library composition: fragmentation → adapters → size selection → PCR |
| Fragments | CE peak classification, purity scoring, dA-tailing evaluation |
| Sanger | Quality trimming, Smith-Waterman alignment, sequence verification |
- Backend: FastAPI + SQLite, Python engines for RE cutting, Cas9 cleavage, GG assembly, library prediction, CE analysis, Sanger alignment
- Frontend: React + Vite + Tailwind SPA served by FastAPI
- Port: 7890 (registered in lab-locations.yaml)
# Backend (auto-reload)
cutscope serve --reload
# Frontend (Vite dev server, proxied to backend)
cd frontend && npm run dev
# Tests (172 tests)
pytest tests/ -v