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rhAmpSeq™ Design Tool

Deep, targeted amplicon sequencing with highly multiplexed panels for sequencing on Illumina® platforms.

  • Generate sequencing panels for a wide range of plant and animal species
  • Minimize primer dimers and maximize multiplexing capability
  • Efficiently analyze on- and off-target CRISPR edit sites
  • Multiplex up to 5000-plex in a single pool

Research-friendly UX

Flexible tool input formats and advanced parameters help you create custom, targeted sequencing panels optimized for your targets:

  • Choose BED or FASTA inputs
  • Optimize for SNP hotspot or CRISPR indel screening
  • Name & save designs for easy reuse and reordering
amplicon sequencing tool

Generating NGS-ready amplicon libraries just got easier

Easy to use sequencing design tool
Design for hotspot target SNPs, indels, and more
Obtain panel designs within 1 hour for most applications*
Easy to use sequencing design tool
Accelerate discovery with quicker, easier ordering
* Larger and more complex panels of 1000+ targets may require a couple days of processing time

rhAmpSeq™ Design Tool tutorial

This tutorial will guide you through the process of using the rhAmpSeq Design Tool, and several of its features. Generate sequencing panels for a wide range of plant and animal species while minimizing primer dimers and maximizing multiplexing capability.

Tailored to your research

Custom rhAmpSeq Panels have been designed and tested in a wide range of animal and plant species and diverse targeted NGS applications, including:

  • Marker-assisted selection and genomic selection in agricultural genetics and breeding
  • Confirmation of on- and off‑target CRISPR gene editing experiments
  • Hotspot panels for oncology, rare and inherited diseases, and other disease research


User guides and protocols

Frequently asked questions

After years of using traditional amplicon sequencing in grapevine, we found that rhAmpSeq’s specificity and evenness of read depth across sites and samples enabled us to multiplex to much higher levels. IDT provided agricultural pricing that enables us to apply 2000 core genome rhAmpSeq haplotype markers to genetic mapping and marker-assisted selection for grape scientists worldwide.

Bruce Reisch
Professor of Grapevine Genetics and Family Genealogist
Cornell University