CRISPR
CRISPR Amplicon Designer
Design PCR amplicons tuned for CRISPR editing and NGS readout.
Design PCR amplicons around CRISPR edits with Tm/GC guardrails and NGS-ready coverage using Omnis Helix, the first Genome IDE.
Tool definition
What the tool is
The Amplicon Designer builds PCR assays around your planned edits, keeping cut and repair zones within high-quality coverage windows.
Decision pressure
Why scientists care
PCR assays are often designed after guides, leading to amplicons that miss indel hotspots or read through repeats.
Genome IDE fit
How the Genome IDE helps
Primer placement relative to cut/peg windows with adjustable offsets
Scoring model
How the algorithm works
Primer candidates are generated with GC, Tm, and secondary structure scoring tuned for genome editing assays.
Evaluation path
Try it in the Genome IDE
Pick a guide, set your preferred amplicon size, and let Helix propose primer pairs with QC badges.
Questions
FAQ
Can I lock GC/Tm ranges?
Yes—set hard constraints and Helix only surfaces primer pairs that satisfy them.
Do you support multiplex PCR?
We flag cross-dimers and overlapping amplicons so you can multiplex safely.
How are exports formatted?
Get CSV, FASTA, and annotated PDF reports aligned to your guide IDs.