NuGEN - Unique Dual Indexes Library Preparation for Next Generation Sequencing

Get more accurate data and eliminate mis-assigned reads due to index hopping!


What is index hopping?

Index hopping is a sequencing phenomenon where the barcode that has been attached to a specific library molecule (read) gets changed to another barcode. This leads to a mis-assignment of that read to the wrong sample.  Index hopping has been shown to occur at a higher frequency in patterned flow cell sequencing platforms, such as the HiSeq 3000, HiSeq 4000, NovaSeq, with errors ranging from 0.1-2%.


What is the solution?

Illumina recommends careful cleanup of final library preparation for next generation sequencing to minimize barcoded primer carryover, proper storage of unpooled libraries at -20°C, pooling of libraries immediately before sequencing and using unique dual indexing pooling combinations.  With NuGEN’s Unique Dual Indexes (UDI), these precautions can be taken with the additional advantage that ligation occurs earlier in the workflow, minimizing the chance of index hopping. 

With NuGEN’s UDIs, use of an additional index can enable detection and eliminate mis-assigned reads from a dataset. This is particularly critical in applications that require high sensitivity, and it improves accuracy of sample assignment in any experiment.

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NuGEN offers up to 384 Unique Dual Indexes.  They are conveniently configured in a pre-plated format as 96 unique barcode pairs, so manual preparation of barcode pairs is completely eliminated. Simply add the adaptor to the sample and ligate.  Each sample will have index1 and index2 barcodes that are completely unique from all other samples on the plate.

The following NGS library preparation systems are available with NuGEN's Unique Dual Indexes (UDI):


Ovation® Ultralow Library System V2

  • A simple, fast and scalable solution for producing libraries that can be used for a broad range of next generation sequencing applications
  • Contains a proprietary DimerFree technology that allows for efficient library preparation with virtually no adaptor dimers even at input levels ranging as low as 10 pg to 100 ng

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Celero™ DNA-Seq Library System

  • Faster library preparation for Illumina sequencers with reduced hands-on time: No adaptor or template dilution and no post- ligation purification
  • One kit, two workflows: PCR and PCR-free can be performed with the same kit, providing flexibility and reducing the number of kits that need to be purchased and stored
  • Simplified library pooling: NuQuant provides molarity without the need for costly and time-consuming methods

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Universal Plus mRNA-Seq

  • A comprehensive solution for mRNA sequencing with the unique option to eliminate unwanted transcripts from the library
  • Broad dynamic input range from 1 ug to as low as 10 ng, enables access to previously inaccessible low input samples
  • Efficient library construction with minimal adaptor dimers enabled by proprietary DimerFree technology
  • Customizable transcript depletion with AnyDeplete maximizes informative data from mRNA sequencing

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Trio RNA-Seq

  • A highly sensitive whole transcriptomics solution that is ideally suited for applications with low abundance transcripts, such as detection of viral transcripts or biomarker assessment in liquid biopsy samples.
  • Consistent performance from wide input range - High quality data from as low as 500 pg
  • Unbiased transcript coverage
  • Excellent results from FFPE and/or degraded samples

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