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xGen™ NGS Adapters & Indexing Primers for Illumina® sequencing

High-quality stocked and customizable options

Adapters & indexing primers are a key component of NGS library preparation workflow. Whether your project requires a basic indexing solution or a more sophisticated design for higher accuracy, we have the products and expertise to deliver the right solution.

xGen NGS—made to differentiate.


  • IDT is the industry standard for both ligation-based and PCR-based indexing solutions
  • A comprehensive offering of high-purity adapters and primers for Illumina sequencing
  • Trusted customer support
  • Complete customizability

Table 1. Recommended adapters and indexing primers for Illumina sequencing based on compatibility with library prep methods.

 Full-length adapters Indexing primer options
Indexing strategy UDI + UMI   UDI    CDI  Normalase™-UDI* Normalase-CDI*
xGen Broad-Range RNA Library Prep Kit   
xGen RNA Library Prep Kit   
xGen DNA Library Prep (MC or EZ) Kit   
xGen DNA Library Prep (MC or EZ) UNI† Kit      
xGen ssDNA & Low-Input DNA Library Prep Kit   
xGen Methyl-Seq Library Prep Kit   
xGen cfDNA &FFPE DNA Library Prep Kit     

* Index primers are also used for Pre-Hyb Normalase Workflow

† Note: the UNI kit supports indexing by ligation, so either full-length (UDI-UMI) or stubby adapter + UDI primers can be used. All other library prep kits only support indexing by PCR

For information on the xGen Normalase Module, click here.

Figure 1. Plate combinations for 1536 UDI primer pairs. Each 96-well plate is sold in a set of four plates. For 1536 UDI primers, order Set 1, 2, 3, and 4.

For plate layouts of each of the 16 UDI plates offered see the xGen™ Normalase™ Indexing Primers quick reference guide.

Custom Adapter Configurator tool

Use the Custom Adapter Configurator tool to design indexing solutions for use with Illumina sequencing platforms, to take your research to the next level. These configurable options include library prep method, configuration, attachment style, indexing strategy and number of indexes, amount, delivery format, and whether to include modifications or TruGrade™ processing. The tool allows you to select adapters for immediate purchase through our online cart or request customer support for assistance if you have more complex requirements for your design.

Note: We suggest to avoid using custom adapters (such as those through the Custom Adapter Configurator Tool) and off-the-shelf, stocked adapters together in the same project. Please contact us for further assistance.

TruSeq™–Compatible Full-length Adapters

Each sequence design includes duplexed adapters, delivered in Duplex Buffer (IDT), and available in tubes or plates.

* Price per number of adapters selected. Addition of methylation and/or TruGrade processing will incur an additional fee.

TruSeq™–Compatible Stubby Adapter and Indexing Primers

Each sequence design includes duplexed adapters designed to be compatible with ligation-based library prep, delivered in Duplex Buffer (IDT) and provided in tubes, as well as a primer mix delivered in IDTE (1X TE), pH 8, available in plates.

* Price per number of adapter-primer sets selected. Addition of methylation and/or TruGrade processing will incur an additional fee.

Nextera™–Compatible Indexing Primers

Each sequence design includes a primer mix designed to be compatible with transposase-based library prep, delivered in IDTE (1X TE), pH 8, available in plates.

*Price per number of primer sets selected. Addition of TruGrade processing will incur an additional fee.

TruSeq™–Compatible Indexing Primers

Each sequence design includes a primer mix designed to be compatible with ligation-based library prep, delivered in IDTE (1X TE), pH 8, available in plates.

* Price per number of primer sets selected. Addition of TruGrade processing will incur an additional fee.

Additional fees for methylated bases

Additional fees for TruGrade processing

If ordering >384 sequences, please use this request form.

TruSeq® and Nextera® are registered trademarks of Illumina, Inc., used with permission. All rights reserved.

For customers who wish to purchase the legacy Swift 2S adapters, Swift indexing primers, or xGen Methyl UDI-UMI adapters, please contact us today.

Product details

Considerations when selecting an adapter and primer design

IDT provides extensive solutions for stocked indexing solutions. Adapters are available with single index, unique dual index (UDI), and unique molecular identifiers (UMI) found in the IDT xGen UDI-UMI indexes (Figure 2). In addition, the adapters can be designed to include:

  • Index lengths of 8 nt or 10 nt
  • Combinatorial or unique dual indexes (CDI or UDI)
  • Multiplex capacity up to 1536 unique indexes
  • Indexing primers designed for performing enzymatic library normalization using our proprietary Normalase technology.

In addition to the stocked products, IDT provides the ability for even greater flexibility and control, by using the Custom Adapter Configurator tool to guide you through designing your own Custom NGS Adapters.

Figure 2. Examples of adapter designs. A variety of NGS adapter designs are available from IDT. When selecting or designing adapters, consideration must be given to the intended application, multiplexing needs, specification requirements, and analysis methods.

Sample indexing

Sample indexes (or indices) enable multiple samples to be sequenced together (i.e., multiplexed) on the same instrument flow cell or chip. Each sample index, typically 8–10 bases, is specific to a given sample library and is used for de-multiplexing during data analysis to assign individual sequence reads to the correct sample. Predesigned indexes from IDT are balanced to prevent GC bias and color-balanced for 2- and 4-color Illumina instruments. Adapters and primers may contain single or dual sample indexes depending on the number of libraries combined and the level of specification desired. Illumina recommends using unique dual indexes (UDIs) as a method to mitigate errors introduced by index-hopping. UDIs are particularly important when using instruments with patterned flow cells, such as the NovaSeq® system from Illumina.

IDT provides several indexing options with its Custom NGS Adapters. These include both IDT and Illumina 8- and 10-base index series, as well as the ability to upload your own index files.

Molecular barcoding

Unique molecular identifiers (UMIs) provide reliable error correction. UMIs are short sequences that incorporate a unique barcode onto each molecule within a given sample library.

  • UMIs are used to identify PCR duplicates. PCR duplicates created during library amplification steps will share the same insert and UMI tag.
  • UMIs have also been shown to reduce the rate of false-positive variant calls and increase variant detection. By incorporating individual barcodes on each original DNA fragment, variant alleles present in the original sample (true variants) can be distinguished from errors introduced during library preparation, target enrichment, or sequencing. Any identified errors can be removed by bioinformatics methods before final data analysis.

Adapters that contain UMIs, such as the xGen UDI-UMI Adapters, are available with a UDI design for identification of low-frequency variants. IDT Custom NGS Adapters can also be configured with UMIs.

Adapter manufacturing

Stringent manufacturing methods are critical for producing high-quality NGS adapters. Substandard manufacturing practices can lead to low-purity adapters or adapter cross-contamination, either of which will negatively impact sequencing results. The IDT proprietary TruGrade™ process uses state-of-the-art synthesis and purification methods, designed specifically for NGS adapters. IDT also offers GMP ISO 13485 grade adapter manufacturing for research applications.

In addition to stringent manufacturing methods, IDT also performs functional NGS testing on each new batch of stocked adapter and indexing primer products to ensure they produce sequencing libraries that meet our high-quality standards.

Our leadership in NGS adapter synthesis made us the clear choice when Illumina sought a partner to develop the next generation of indexed adapters to improve sample multiplexing. These adapters contain Illumina’s unique dual indexes (UDIs), which mitigate sample misassignment due to index hopping. We manufacture UDI adapters for Illumina and are also licensed to sell your own custom designs containing these UDI sequences.

For more information, or to order custom adapters, please contact us.

Indexing Option xGen UDI-UMI Adapters xGen Stubby Adapter and UDI Primers xGen Normalase UDI Primers xGen UDI Primers xGen Normalase CDI Primers xGen CDI Primers Custom NGS adapters
Configuration UDI-UMI UDI UDI UDI CDI CDI Single index, combinatorial dual indexing, UDI, or UDI-UMI
Sample index length 8 base, unique sample indexes 8 base, unique sample indexes 10 base, unique sample indexes Both 8 and 10 base available, unique sample indexes 8 base indexes 8 base indexes Configurable
Concentration 15 µM  15 µM (Stubby adapter),
10 µM ( each primer)
Proprietary 20 µM total (10 µM each Primer)
  • xGen UDI Primers Plate 1, 8nt
  • xGen UDI Primers, 16 rxn
  • xGen UDI 10nt Primers (all)
12 µM total (6 µM each primer)
  • xGen UDI Primers Plate 2, 8 nt
Proprietary12 µM total (6 µM each primer after arraying) 15 µM (Adapter),
20 µM total (10 µM each Primer)
Shipping container 96-well plates, single use Tubes (Stubby Adapter),
Single-use plates (Primers)
96-well plates, single use 96-well plates, single use

UDI 10 nt Primers (2nm) plates are bulk/multi-use
Tubes for each i7 and i5 index Tubes for each i7 and i5 index Tubes, Matrix® plates†, or single-use plates
Reactions 1 reaction per adapter 1 reaction per primer pair 1 rxn per primer pair 1 rxn per primer pair for 96-well plates, single use 1 rxn per primer pair 1 rxn per primer pair Varies
Illumina platform compatibility 2- and 4- color systems 2- and 4- color systems 2- and 4- color systems 2- and 4- color systems 2- and 4- color systems 2- and 4- color systems Designs for any application

Choose from a variety of options that personalize the adapters to your NGS workflow for Illumina sequencing. Order Custom NGS Adapters when you need to:

  • Scale up your experiments—get the delivery format (volume, plate, single-use) and volume-pricing that best suit your NGS study.
  • Expand your set of barcodes to increase sample throughput—augment limited sets of stocked adapters. Our design tool will support uploading up to 2000 custom index sequences!
  • Supplement commercial library kit components—create your own custom library prep workflow that fits your experimental design.

The Custom Adapter Configurator tool helps you design the adapters best suited to your experiments by walking you through these choices:

  • Library prep method
  • Configuration (SI, CDI, UDI, UDI-UMI)
  • Attachment style
  • Indexing strategy
  • Number of indexes
  • Size (reaction number or nmol)
  • Delivery format (tubes, plates)
  • Methylated/unmethylated
  • TruGradeTM processing

Table 2. Suggested barcode configuration based on NGS application.

ApplicationBest choiceAlternatives
Germline characterization
SNPs, indels, crude CNV; no concern of sample crosstalk
Germline characterization where sample crosstalk is important
Translational research, inherited genetics, infectious disease research
Low-level mutation detection, down to ~1% frequency
Cancer, mosaicism, other diseases where somatic mutations are important

Frequently asked questions

TruSeq® and Nextera® are registered trademarks of Illumina, Inc., used with permission.  All rights reserved.

GMP refers to products manufactured under ISO 13485: 2016 QMS. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations for their legal marketing.