PlannerOpen
CRISPR / Prime Planner
Geometry-aware planning with RT/PBS helpers, printable diagrams, and saveable plan links.
- Paste target + guides
- Describe edit (sub, ins, del)
- Export PDF or share link
Documentation
Operate Helix Tools with confidence.
Short, task-focused docs for planning CRISPR/Prime edits, scanning PCR products, and running batch campaigns.
Nothing is persisted until you hit Save & Share. Local history is kept in your browser for quick recall.
Runtime
Browser + API
Exports
PDF, CSV
Batch
CSV in/out
Tooling
Product surfaces
Inputs, outputs, and what success looks like for each surface in the suite.
PCROpen
PCR Product Finder
Fast amplicon sizing for primer pairs with GC%, Tm, and off-target flags.
- Enter left/right primers
- Scan against your sequence
- Review flagged amplicons
BatchOpen
Batch Edit Planner
Upload CSVs for multi-edit programs and download campaign-ready outputs.
- CSV in for targets + edits
- Parallel plan generation
- CSV/PDF exports
PrimersOpen
Primer Quality Checker
Single or batch primer QC with clamp rules, dimers, and ordering sanity checks.
- One-off or list input
- Clamp/Tm heuristics
- Quick copy/export
Guided flows
Quick starts
Follow these when onboarding a teammate or verifying a new release.
Step-by-step
Plan a prime edit
- Open the CRISPR / Prime Planner and paste your target + spacer.
- Describe the edit (substitution, insertion, deletion) and let geometry update live.
- Validate RT/PBS helpers, distances, and warnings.
- Export a PDF or click Save & Share to create a link.
Step-by-step
Scan PCR primers
- Drop in forward + reverse primers on the PCR Product Finder.
- Review GC%, Tm, and product sizes; flagged rows surface off-target risk.
- Export CSV for ordering or drop back into Planner to design edits nearby.
Step-by-step
Run a batch campaign
- Download the CSV template from Batch Edit Planner and fill targets + edits.
- Upload the file; the table previews any malformed rows before compute.
- Export combined CSV/PDF outputs for the full campaign once checks are green.
Reference
Operating notes
Keep these nearby when you deploy or file issues.
Data + privacy
Plans stay in your browser history until you click Save & Share. Saved plans live behind unique IDs; remove them from history locally anytime.
APIs
Frontend calls /api/plan for single designs and /api/plans for saved payloads. Responses are JSON; PDF exports happen client-side.
Support
File an issue on GitHub or attach sample input when reporting a bug. Include sequence snippets, primer pairs, and the tool you used.