Adapters for Next Generation Sequencing

High quality adapters that meet the ever-expanding needs of researchers using NGS

Adapters are a key component of the next generation sequencing (NGS) workflow. Whether your project requires a basic adapter or a sophisticated design for higher accuracy, IDT has 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 xGen Dual Index UMI Adapters, xGen Stubby Adapter and Unique Dual Index Primers, and a Custom Adapter Configurator tool that guides you through design of Custom NGS Adapters. Below we describe some of the design considerations you will want to take into account.

Sequences for specific NGS platforms: During library preparation, adapters are attached (by ligation, PCR, or tagmentation) to the fragments of each sample library. Adapters include platform-specific sequences for fragment recognition by the sequencer: for example, the P5 and P7 sequences (Figure 1) enable library fragments to bind to the flow cells of Illumina platforms. Each NGS instrument provider uses a specific set of sequences for this purpose. IDT manufactures adapters for all major NGS platforms.

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 6–10 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. Adapters may contain single or dual sample indexes depending on the number of libraries combined and the level of accuracy 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.

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 the highest levels of error correction and accuracy. UMIs are short sequences, often with degenerate bases, that incorporate a unique barcode onto each molecule within a given sample library. UMIs have been shown to reduce the rate of false-positive variant calls and increase sensitivity of 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 Dual Index UMI Adapters, are available with a UDI design for detection 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 grade adapter manufacturing for clinical applications.

Choose IDT adapter products based on the flexibility your experimental workflow requires. Click on the xGen Dual Index UMI Adapters—Tech Access, the xGen Stubby Adapter and UDI Primers, or the Custom NGS Adapters headings in Table 1 to review product offerings. The Custom NGS Adapters provide a step-by-step tool to help you configure adapters best suited for your research.

 

SpecificationsxGen Dual Index UMI Adapters—Tech AccessxGen Stubby Adapter and UDI PrimersCustom NGS adapters
ConfigurationUDI-UMIUDIsingle index, combinatorial dual indexing, UDI, or UDI-UMI
Sample index length8 base, non-redundant sample indexes8 base, non-redundant sample indexesConfigurable
Concentration15 µM 15 µM (Stubby Adapter), 20 µM total (10 µM each Primer)15 µM (Adapter), 20 µM total (10 µM each Primer)
Shipping containerTubes, plates Tubes (Stubby Adapter), 96-well plates (UDI Primer Pairs)Tubes, plates, or single-use plates
ReactionsVaries1 reaction per primer pairVaries
Adapter modificationsAvailableMethylated for bisulfite sequencing*Available
Illumina platform compatibility2- and 4-color platforms2- and 4-color platformsDesigns for any application

* For bisulfite sequencing, see our FAQ for additional information.

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 Lotus DNA 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 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 our selection of pre-configured, ready-to-ship xGen adapters and indexing primers in single-use plates.

 

TruSeq–Compatible Full-length Adapters

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

 Quantity
Price per index*
Adapter configuration2 nmol8 nmol24 nmol16 rxn96 rxn
Single Index (SI) ConfigurationCHF 96.00 CHFCHF 191.00 CHFCHF 391.00 CHFCHF 73.00 CHFCHF 173.00 CHF
Combinatorial Dual Indexing (CDI) ConfigurationCHF 68.00 CHFCHF 96.00 CHFCHF 196.00 CHFCHF 51.00 CHFCHF 90.00 CHF
UDI ConfigurationCHF 146.00 CHFCHF 291.00 CHFCHF 581.00 CHFCHF 113.00 CHFCHF 270.00 CHF
UDI-UMI ConfigurationCHF 146.00 CHFCHF 291.00 CHFCHF 581.00 CHFCHF 113.00 CHFCHF 270.00 CHF

* 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, 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.

 Quantity
Price per index*
Adapter configuration2 nmol8 nmol24 nmol16 rxn96 rxn
Single Index (SI) ConfigurationCHF 68.00 CHFCHF 132.00 CHFCHF 278.00 CHFCHF 52.00 CHFCHF 126.00 CHF
Combinatorial Dual Indexing (CDI) ConfigurationCHF 40.00 CHFCHF 56.00 CHFCHF 132.00 CHFCHF 34.00 CHFCHF 52.00 CHF
UDI ConfigurationCHF 90.00 CHFCHF 192.00 CHFCHF 382.00 CHFCHF 72.00 CHFCHF 186.00 CHF

* 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 delivered in IDTE (1X TE), pH 8, available in plates.

 Quantity
Price per index*
Adapter configuration2 nmol8 nmol24 nmol16 rxn96 rxn
Single Index (SI) ConfigurationCHF 52.00 CHFCHF 136.00 CHFCHF 280.00 CHFCHF 34.00 CHFCHF 56.00 CHF
Combinatorial Dual Indexing (CDI) ConfigurationCHF 28.00 CHFCHF 68.00 CHFCHF 140.00 CHFCHF 18.00 CHFCHF 28.00 CHF
UDI ConfigurationCHF 52.00 CHFCHF 136.00 CHFCHF 280.00 CHFCHF 34.00 CHFCHF 56.00 CHF

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

Additional fees for methylated bases

 Quantity
Price per index*
Style2 nmol8 nmol24 nmol16 rxn96 rxn
TruSeq™–Compatible Stubby Adapter/Indexing PrimersCHF 68.00 CHFCHF 86.00 CHFCHF 112.00 CHFCHF 56.00 CHFCHF 80.00 CHF
TruSeq™–Compatible Full-length AdaptersCHF 68.00 CHFCHF 85.00 CHFCHF 113.00 CHFCHF 56.00 CHFCHF 78.00 CHF

Additional fees for TruGrade processing

 Quantity
Price per index*
Style2 nmol8 nmol24 nmol16 rxn96 rxn
Nextera™–Compatible Indexing PrimersCHF 34.00 CHFCHF 102.00 CHFCHF 136.00 CHFCHF 28.00 CHFCHF 40.00 CHF
TruSeq™–Compatible Stubby Adapter/Indexing PrimersCHF 46.00 CHFCHF 102.00 CHFCHF 170.00 CHFCHF 34.00 CHFCHF 96.00 CHF
TruSeq™–Compatible Full-length AdaptersCHF 117.00 CHFCHF 157.00 CHFCHF 181.00 CHFCHF 98.00 CHFCHF 147.00 CHF

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

(Visit the IDT Usage, warranty & licensing page for specific information about Illumina trademarks.)