Your product is now available from Integrated DNA Technologies.
Many of the Swift products you have grown to love are now part of our new complete portfolio, xGen™ NGS. Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions.
xGen NGS—made for you.
Unsure of what products are available? Or, perhaps you’d like guidance on which products are compatible? If so, try our xGen NGS Solutions Builder Tool today.
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
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 TruGradeTM 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 our Scientific Application Support team (email@example.com) for further assistance.
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.
TruSeqTM–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.
NexteraTM –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.
TruSeqTM–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.
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 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.
Figure 1. 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 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.
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.
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 TruGradeTMprocess 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.
These two specific products were brought into the xGen portfolio from Swift Biosciences. To preserve the configuration of the products that support Swift's legacy customers, we did not alter the concentration or any other specifications, we only rebranded these products using new names.
NGS libraries constructed using the stocked xGen Stubby Adapter–UDI Primers are Illumina TruSeq®-compatible and should be sequenced on an Illumina platform with our UDI-UMI Adapters and Normalase™ Indexing options.
Our Custom Adapter Configurator Tool helps you to create custom indexing options for not only Illumina TruSeq®- compatible workflows, but also Illumina Nextera®-compatible workflows.
TruSeq® and Nextera® are registered trademarks of Illumina, Inc., used with permission. All rights reserved.
No, Normalase PCR requires replacing your amplification primers to condition your libraries for the downstream enzymology. Reagent R5 replaces standard library amplification primers for those libraries indexed by adapter ligation.
Reagent R6 with xGen™ Normalase CDI primers, or Reagent R7 with Normalase UDI primers, replace your indexing primers for libraries indexed by PCR.
The amount of xGen UDI-UMI Adapters you use depends on the library prep workflow and the amount of starting sample used to perform library prep. We recommend checking your specific protocol for the optimal amount of adapter to use.
For the xGen DNA Library Prep Kits, use 5 µL of xGen UDI-UMI Adapters (diluted according to the table below) for the ligation reaction.
The xGen™ RNA Library Prep Kit includes a stubby adapter in the workflow so the stocked UDI-UMI adapters are not compatible with those kits.
For customers using homebrew, or other commercial RNA-seq workflows that utilize TA-ligation, these UDI-UMI adapters are compatible. However, it is important to note that stranded RNA-seq libraries constructed using xGen UDI-UMI Adapters have the insert strandedness flipped (i.e., to the opposite strand) when compared to standard Illumina TruSeq™ adapters. As such, this strand flip must be handled during data analysis.
Disclaimer: TruSeq™ and Nextera™ are registered trademarks of Illumina, Inc., used with permission. All rights reserved.