KAPA RiboDesigner

Design your own custom rRNA depletion probes—no bioinformatics expertise required!

Learn how
KAPA RiboDesigner banner - with RNA strand and text

A powerful, flexible new probe design solution for custom depletion of rRNA

KAPA RiboDesigner is a powerful, flexible new probe design solution for the targeted depletion of rRNA from any species for which the rRNA sequences are known, including multi-species RNA samples.

Once the probes are synthesized, RNA-seq libraries are then prepared by incorporating the custom probes into the robust KAPA RNA HyperPrep Kit with RiboErase (HMR) in place of the provided HMR probes, which target only human/mouse/rat rRNA.

KAPA RiboDesigner may also prove useful in other RNA-seq applications, such as the depletion of highly abundant  transcripts from specific tissues or metagenomic samples.

Learn how

Advantages of KAPA RiboDesigner over manual probe design methods include:

  1. No bioinformatics expertise is required.
  2. KAPA RiboDesigner simultaneously designs probes targeting all rRNA from provided annotated genomes, and is effective for multi-species samples.
  3. The algorithm minimizes the total number of probes by avoiding the selection of multiple probes for redundant sequences ─ such as multiple copies of rRNA genes within a single genome, or similar rRNA genes in mixed-species samples.
  4. KAPA RiboDesigner selects high-quality probes by using a sliding-window approach, where the window moves along the sequence from beginning to end. At  each location, multiple probes are evaluated for GC content, sequence complexity, and possible off-target effects; then, the most optimal probe is selected.

Efficient, reproducible rRNA depletion from bacterial RNA

Figure 1. Bacterial rRNA is efficiently depleted (>98%) using probes selected by KAPA RiboDesigner. When probes selected by KAPA RiboDesigner were tested on total RNA from
E. coli  (Panel A) and from a mixture of RNA from 8 bacterial species (Panel B), the rRNA content was reduced to ~2% from the original ~95% and ~92%, respectively. For both sample types, custom probes were incorporated into the KAPA RNA HyperPrep Kit with RiboErase (HMR) for RNA-seq library preparation, followed by sequencing on an Illumina NextSeq 500 sequencing instrument.

Robust, reproducible gene expression

Figure 2: Highly correlated gene expression between rRNA-depleted and non-depleted E. coli samples. Gene expression patterns were highly reproducible (94% correlation) for all three replicates, indicating that rRNA depletion using custom probes has minimal impact on the assessment of gene expression. Both the X axis and Y axis represent gene expression in log2 format.

Learn how KAPA RiboDesigner can help you with your NGS project

If you have questions, or if you would like to learn how KAPA RiboDesigner can help you with your NGS project, please fill out the form below and a customer support specialist will contact you to discuss the details:

Upon your RiboDesigner request submission:

  1. Submit a KAPA RiboDesigner request online
  2. Roche Bioinformatician will discuss your needs and design the custom probes
  3. Purchase the custom probes from an oligo vendor of your choice
  4. Perform the rRNA depletion workflow using the KAPA RNA HyperPrep RiboErase (HMR) kit
  5. Roche Bioinformatician will follow up and ensure your success