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 Helix Studio, the first Genome IDE.
System of Record →Section 1
What the tool is
The Amplicon Designer builds PCR assays around your planned edits, keeping cut and repair zones within high-quality coverage windows.
Section 2
Why scientists care
PCR assays are often designed after guides, leading to amplicons that miss indel hotspots or read through repeats.
Section 3
How Helix solves it
Primer placement relative to cut/peg windows with adjustable offsets
Section 4
How the algorithm works
Primer candidates are generated with GC, Tm, and secondary structure scoring tuned for genome editing assays.
Section 5
Try it in Helix Studio
Pick a guide, set your preferred amplicon size, and let Helix propose primer pairs with QC badges.
Section 6
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.