NGS UDI Primer Sets – Unique Dual Index for Illumina | Eurofins Genomics
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    NGS UDI Primer Sets

    Prevent misassignment. Optimize multiplexing. Sequence smarter.

    Order now
     

    NGS UDI Primer Sets

     

    Our NGS UDI Primer Sets use advanced 12-base Unique Dual Indexes (UDIs) with high edit distances for maximum demultiplexing precision. Engineered for compatibility with Illumina platforms, these primers are optimised to reduce cross-talk and to deliver unmatched sequencing reliability. Ideal for high-throughput applications, complex multiplex setups, rare somatic variant analysis and RNA-sequencing. NGS UDI Primer Sets are delivered in a full-skirted 96-well PCR plate with a pierceable foil seal. Each primer pair has a concentration of 10µM provided in bidest water in 10µl for single use. Enter the quantity you need and click "Add to Cart".

     

    Validated In-House

     

    ISO 13485 Certified

     

    Ready-to-ship 96-well plates

     

    Smarter Primers. Cleaner Data.

    UDI primers that do the heavy lifting, so your NGS results speak for themselves.

    Order now
     

    The problem

     

    NGS Multiplexing Without a Safety Net

     

    Multiplexing is a smart way to reduce sequencing costs — but it comes with risks.

     

    If you're experiencing any of the following issues, you're not alone:

     

    ❌ Misassignment of reads due to index hopping & cross-contamination

    ❌ Sequencing waste of unusable data

    ❌ Incorrect data interpretation and false positive data

    ❌ Low sensitivity, high limits of detection, unrobust sequencing assays

    ❌ Long delivery times or inflexible set combinations

     

    Scientists today are under pressure to deliver clean, reproducible data — and compromised index primers are a common root cause of unreliable sequencing results.

     

    OUR SOLUTION

     

    UDI Primers That You Can Trust

     

    Eurofins Genomics’ NGS UDI Primer Sets offer a reliable way to safely multiplex without compromise:

     

    ✔️  12-base unique dual indexes (UDI) – long and safe 

    ✔️  ≥4 base edit distance – minimizes misassignment

    ✔️ Ultra-low cross-contamination – Average risk between two UDI pairs are < 0.4 reads when sequencing 10M reads 

    ✔️ NGS performance-verified in-house

    ✔️ ISO 13485 medical device certification for in vitro diagnostic use

    ✔️ Compatible with Illumina TruSeq & NEB adapters 

    ✔️ Scalable: Combine 4 x 96 sets to reach 384 indices 

    ✔️ Transparent pricing: Only €299 per 96-primer set

     

     

    Proven Performance

     

    • 99.9986% of reads correctly assigned in Illumina NovaSeq 6000 tests
    • Validated across 96 unique index combinations
    • Available in ready-to-ship 96-well plates – combine to 384 UDIs

     

    Read the full Application Note →

    Why Double Indexing Matters

     

    Think of your sequencing pool like a shared washing machine. You toss in dozens of samples — and hope everything comes back to the right owner.

    • Single indexes = Risky laundry
    • Poorly designed UDIs = Mismatched socks
    • Index hopping = Total chaos
    • Unique Dual Indexing means every DNA fragment gets two matching labels — dramatically reducing errors, contamination, and frustration.
     

     

    Product Specifications

     

    Feature Details
    Format 96-well plate (96 primer pairs)
    Index length 12 nucleotides
    Edit distance 4 bases
    Compatibility Compatible with Illumina TruSeq & NEB adapters
    Quality NGS performance-verified in-house & ISO 13485 medical device certification
    Cross-contamination Average risk of misassigned reads between two UDI pairs of < 0.4 reads when sequencing 10M reads
    Purification Proprietary method, no HPLC
    Price From €299 / set
     

     

     

     



    NGS UDI Primer Set 96-01
    UDP0001-0096

     


    96 primer pairs for 96 reactions


    Click here to download plate assignment with u7 and u5 index primer sequences.*

     
     
     
    Quantity:

     
     
    Price:
    299,00 €
     
         
         



    NGS UDI Primer Set 96-02
    UDP0097-0192

     


    96 primer pairs for 96 reactions


    Click here to download plate assignment with u7 and u5 index primer sequences.*

     
     
     
    Quantity:

     
     
    Price:
    299,00 €
     
         
         



    NGS UDI Primer Set 96-03
    UDP0193-0288

     

    96 primer pairs for 96 reactions


    Click here to download plate assignment with u7 and u5 index primer sequences.*

     
     
     
    Quantity:

     
     
    Price:
    299,00 €
     
         
         



    NGS UDI Primer Set 96-04
    UDP0289-0384

     

    96 primer pairs for 96 reactions


    Click here to download plate assignment with u7 and u5 index primer sequences.*

     
     
     
    Quantity:

     
     
    Price:
    299,00 €
     

     


    * For information on which u5 index orientation to use (forward or reverse complement), please refer to the following Illumina page:

     

    https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Overview.htm

     

     

     

    Information for the use of 12 bp UDI sequences for sequencing on MiSeq systems can be found here.

     

     

     

     

     

    Get Started
    Ready to bring clarity to your sequencing results?

     

    • €299 per set
    • One-click ordering
    • Available with rapid delivery
    • Talk to our smart 24/7 assistant.

      Call us anytime at +49 30 219 244 13
      Let´s discuss product options and specifications – in English or German.

     

    Built for Precision. Backed by Science.

    Tested, certified, and trusted by top-tier labs across Europe.

    Order now
     

    Explore More

    Deepen your understanding with curated resources

    Whether you need technical validation, inspiration, or application know-how – these links lead the way.

     

    Application Note NGSgrade Oligos 2.0 

    Blog: Oligonucleotides for Diagnostics

    Blog: How to do NGS 50% faster

    Blog: Meet the team

    Blog: NGS UDI Primer Sets for multiplexed sequencing: Eliminate index misassignment

     

     

     

     

     

     

    Frequently Asked Questions (FAQ)

     

    Quick answers to common concerns: We know that time matters. Here are some of the most common questions we get – and how our NGS UDI Primer Sets can help.

     

     

    1. Can I use these primers for RNA-seq?
      Yes. They are ideal for RNA-seq, microbiome analysis, and all Illumina-based NGS workflows.

    2. Are the sets combinable??
      Yes, you can freely combine 4 x 96 UDI sets for up to 384 unique index pairs.

    3. How are the primers tested?
      Each batch undergoes NGS-based QC in our in-house lab to ensure performance and purity.

    4. Is cross-contamination really that low?
      Yes. With a verified rate of 0.0014%, we outperform most market standards 10x.
      What if it doesn’t work? We stand behind our product. If your results are not as expected, we’ll work with you through our dedicated customer support to investigate. This includes free replacement, reruns, or refund where applicable. Your success is our priority.

     

     

     

    >> More FAQ's Here

     

     

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