NimbleDesign Software

NimbleDesign Software

NimbleDesign is a free online tool which enables you to quickly and easily design custom SeqCap or HEAT-Seq Choice Designs. NimbleDesign software capitalizes on years of design experience which has resulted in our empirically optimized probe database and design process for proven probe selection. This web-based application provides you with 24/7 access with easy setup in designing your probe sets for your custom SeqCap and HEAT-Seq designs for human research applications.

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  • Rapid turnaround time for custom designs. Select your genomic targets using easy step-by-step instructions; develop multiple designs in parallel for quick review and selection of the best design within a few hours.
  • Maximize your convenience with an easy workflow. NimbleDesign provides you with 24/7 access with easy setup for creating and approving your custom human target enrichment designs with Roche Sequencing.
  • Discover more variants through our proven industry leading design algorithm*. In SeqCap applications benefit from the superior capture efficiency of our design informatics and 2.1M overlapping probes to ensure the highest uniform coverage to truly discover more.
  • Rapidly configure custom molecular inversion probe (MIP) panels. Leverage the data-driven HEAT-Seq Choice and Ultra Choice databases to create custom panels of up to 20,000 probes for human genetics and cancer research applications.

*Clark M, et al. Nat. Biotech. 2011; doi:10.1038/nbt.1975 (see Nature Biotechnology article)



  • Intuitive User Interface from Start to Finish
    Follow clear, simple instructions to create one design or many in parallel for your target region of choice.
  • Flexible Input
    Choose from a broad list of commonly used gene identifiers to retrieve annotation for your review. In addition to coordinate entry, input a long list of gene names or look up genes via the search tool to add target regions for your design.
  • Comprehensive Design Features
    Design to target the human or mouse genomes and choose to create or modify DNA or RNA designs.

Performance Data


Figure 1: Design comparison between SeqCap EZ Choice Enrichment System and Competitor A Design Software. A 3.51Mb region on Chromosome 18 was targeted to compare probe coverage across design platforms. NimbleDesign probes covered 79.3% of the target region (2.79 Mb of target) compared to a coverage of 50.2% (1.77 Mb of target) by Competitor A design software. Note: Probe design used standard design parameters for both NimbleDesign and Competitor A software. Coordinate files from each design was uploaded to SignalMap software to obtain coverage file illustrated above. About 1.05 Mb of coverage space was unique to the NimbleDesign platform that was not covered by the Competitor A software.