xGen™ NGS Adapters & Indexing Primers - 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.

Regardless of the NGS instrument or application, IDT has been serving the needs of NGS scientists for over 10 years. We are recognized as the leader in adapter synthesis based on our experience in custom oligo manufacturing and our commitment to quality. Additionally, our NGS customers and partners benefit from:

  • A comprehensive adapter offering
  • Innovative designs
  • Trusted customer support
  • Complete customizability

Due to our leadership in NGS adapter synthesis, Illumina chose IDT as its partner to develop the next generation of index adapters to improve sample multiplexing. These adapters contain Illumina’s unique dual indexes (UDIs) that mitigate sample misassignment due to index hopping. IDT manufactures UDI adapters for Illumina and is also licensed to sell your own custom designed adapters containing these UDI sequences. See the press release here.

 

Considerations when selecting an adapter 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 1). 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 NormalaseTM 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.

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 TruGradeTM 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 clinical 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.

Stocked product details

Indexing OptionxGen UDI-UMI AdaptersxGen Stubby Adapter and UDI PrimersxGen UDI PrimersxGen CDI PrimersCustom NGS adapters
ConfigurationUDI-UMIUDIUDICDIsingle index, combinatorial dual indexing, UDI, or UDI-UMI
Sample index length8 base, unique sample indexes8 base, unique sample indexesBoth 8 and 10 base available, unique sample indexes8 base indexesConfigurable
Concentration15 µM15 µM (Stubby adapter),
10 µM ( each primer)
20 µM total (10 µM each Primer)
  • xGen UDI Primers Plate 1, 8nt
  • xGen UDI Primers, 16 rxn
  • xGen UDI 10nt Primers (all)
12uM total (6uM each primer)
  • xGen UDI Primers Plate 2, 8nt
12uM total (6uM each primer after arraying)15 µM (Adapter),
20 µM total (10 µM each Primer)
Shipping container96-well plates, single useTubes (Stubby Adapter),
Single-use plates (Primers)
96-well plates, single use

UDI 10nt Primers (2nm) plates are bulk/multi-use

Tubes for each i7 and i5 indexTubes, Matrix® plates†, or single-use plates
Reactions1 reaction per adapter1 reaction per primer pair1 rxn per primer pair for 96-well plates, single use1 rxn per primer pairVaries
Illumina platform compatibility    2- and 4- color systems2- and 4- color systems2- and 4- color systems2- and 4- color systemsDesigns for any application

 

xGen Stubby Adapter and Unique Dual Index Primer Pairs

Single-use, TA-ligation-ready, stubby Y adapter and indexing primers

Ensure maximum accuracy in your NGS reads with xGen Stubby Adapter and Unique Dual Indexing (UDI) Primer Pairs. A convenient indexing option for a variety of applications from whole-genome to targeted sequencing, the kit provides adapters and 96 unique i5 and i7 primer pairs, compatible with TruSeq™-compatible library prep for sequencing on Illumina instruments.

  • NGS quality control—IDT is unmatched in the industry
  • UDIs—the current standard for data accuracy and confidence
  • Ready to use—stubby Y adapter and indexing primers designed for TA-ligation libraries
  • Easy to get—pre-configured and ready to ship

 

Product Details

xGen Stubby Adapter-UDI Primers are designed for TA-ligation libraries, such as libraries created using the xGen™ DNA EZ Library Prep Kit. The xGen Stubby Adapter is a short Y adapter that can be ligated to fragments with A overhangs generated during library prep. Indexing primers containing unique i5 and i7 indexes as well as P5 and P7 sequences are added to the library via PCR amplification.

The kit contains the stubby adapter and 96 indexing primer pairs with 8 base i5 and i7 indexes. Unique dual indexes (UDIs) enable identification of misassigned reads, so these can be filtered during data analysis to improve accuracy. Adapters and indexing primers are also sold separately.

Custom NGS Adapters

Adapter and indexing primer selections for DNA library prep

Choose from a variety of options that personalize the adapters to your NGS workflow. 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.
  • Supplement commercial library kit components—create your own custom library prep workflow that fits your experimental design.

The IDT 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
  • TruGrade processing

 

Ordering

Use the Custom Adapter Configurator tool to guide you through choices of adapter format and options. These 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.

Need them sooner? Check out IDT's selection of pre-configured, ready-to-ship xGen adapters and indexing primers in single-use plates

For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.