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QIAseq FX DNA Library Kit

All-enzymatic whole genome and hybrid capture library preparation for Illumina instruments with minimal bias

  • Streamlined 2.5-hour workflow for easy automation
  • High library complexity and uniform coverage maximizes interpretable data
  • Unique Dual Index (UDI) adapters available for multiplexing up to 384 samples
  • Fragment size, input amount and batch size customizable to any sequencing experiment
  • Flexible DNA inputs of 20 pg –1 µg

 

Our QIAseq FX technology incorporates an all-enzymatic DNA fragmentation into a streamlined, optimized protocol that doesn’t require additional sample clean-up before adapter ligation. A simple, three-reaction protocol enables straightforward automation of library preparation on various liquid-handling platforms, reducing hands-on time and run-to-run variability. Compatible with Illumina sequencing instruments and available in 24- and 96-sample configurations, when combined with our QIAseq Unique Dual Index Y-Adapter Kits they support multiplexing up to 384 samples. Requiring just 2.5 hours for library prep, and with no need for additional expensive DNA shearing equipment, substantial time and costs are saved.


Want to try the QIAseq FX DNA Library Kit with combinatorial dual indexes for the first time? Request a quote for a trial kit.

Want to try the QIAseq FX DNA Library UDI Kit for the first time? Request a quote for a trial kit.

Need a quote for your research project or would you like to discuss your project with our specialist team? Contact Us

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Cat No./ID: 180310
QIAseq UDI Y-Adapter Kit (24)
£265.00
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Box containing dual bar-coded Unique Dual Sample Index Y-adapters; plate-format for 24 samples

Cat No./ID: 180312
QIAseq UDI Y-Adapter Kit A (96)
£981.00
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Box containing dual bar-coded Unique Dual Sample Index Y-adapters; plate-format for 96 samples; no library preparation reagents included

Cat No./ID: 180314
QIAseq UDI Y-Adapter Kit B (96)
£981.00
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Box containing dual bar-coded Unique Dual Index Y-adapters; plate-format for 96 samples; no library preparation reagents included

Cat No./ID: 180316
QIAseq UDI Y-Adapter Kit C (96)
£981.00
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Box containing dual bar-coded Unique Dual Index Y-adapters; plate-format for 96 samples; no library preparation reagents included

Cat No./ID: 180318
QIAseq UDI Y-Adapter Kit D (96)
£981.00
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Box containing dual bar-coded Unique Dual Index Y-adapters; plate-format for 96 samples; no library preparation reagents included

Cat No./ID: 180473
QIAseq FX DNA Library Kit (24)
Add Software Bundle
£640.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 24 combinatorial dual index adapters with different bar codes (pierceable foil seal, allowing usage of defined parts of plate)

Cat No./ID: 180475
QIAseq FX DNA Library Kit (96)
Add Software Bundle
£2,533.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 96 combinatorial dual index adapters with different bar codes (pierceable foil seal, allowing usage of defined parts of plate)

Cat No./ID: 180477
QIAseq FX DNA Library UDI Kit (24)
£599.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 24 Unique Dual Index Y-adapters

Cat No./ID: 180479
QIAseq FX DNA Library UDI-A Kit (96)
£2,373.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 96 Unique Dual Index Y-adapters

Cat No./ID: 180480
QIAseq FX DNA Library UDI-B Kit (96)
£2,373.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 96 unique dual-index Y-adapters

Cat No./ID: 180481
QIAseq FX DNA Library UDI-C Kit (96)
£2,373.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 96 Unique Dual Index Y-adapters

Cat No./ID: 180482
QIAseq FX DNA Library UDI-D Kit (96)
£2,373.00
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Buffers and reagents for DNA fragmentation (including end repair and A-addition), ligation and library amplification; for use with Illumina instruments; includes a plate containing 96 Unique Dual Index Y-adapters

The QIAseq FX DNA Library Kit is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

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Lower duplication rate
1 ng (all kits including QIAseq FX) or 100 ng (QIAseq FX only) genomic DNA was used as the input in a comparative duplication rate experiment. At 1 ng of input, the QIAseq FX DNA Library Kit performs comparably to mechanical shearing. At 100 ng input, QIAseq FX duplication rates are even lower, approaching the level typically seen from PCR-free workflows.

Other supplier methods: Supplier C: mechanical shearing combined with standard library prep; Supplier N: fragmentase; Supplier I: tagmentation.
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Customizable fragment sizes
The QIAseq FX DNA Library Kit generates customizable, reproducible DNA fragmentation. A Fragmentation of samples using the QIAseq FX DNA Library Kit is highly customizable. Three separate libraries were produced to demonstrate the wide range of fragment sizes possible using the QIAseq FX kit. Libraries shown include inserts approximately 200 (green), 500 (blue) or 1000 (red) bp long. Data were generated using an Agilent® Bioanalyzer.
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No significant differences between coverage of high or low GC genomic regions
With or without PCR, the QIAseq FX DNA Library Kit gives comparable genome coverage to mechanical shearing.

PCR-free library yields from the QIAseq FX DNA Library Kit are highly linear, with the amount of total library generated directly proportional to the amount of input DNA.

Other supplier methods: Supplier C: mechanical shearing combined with a standard library prep.
9
Superior coverage distribution
For this comparative distribution experiment, the input was 100 ng samples of an equimolar mixture of genomic DNA from three bacterial species with vastly different GC contents: Fusobacterium nucleatum with 27% GC; Escherichia coli with 50% GC; and Bordetella pertussis with 67% GC (with the exception of the sample undergoing tagmentation, as only specific input amounts are accepted). The single, narrow peak for the library created with QIAseq FX DNA Library Kit shows that the majority of genomic targets have very similar total coverage depth. This is comparable to DNA fragmented by mechanical shearing.

Other supplier methods: Supplier C: mechanical shearing combined with standard library prep; Supplier N: fragmentase; Supplier I: tagmentation.
9
High Reproducibility
DNA samples with broad GC contents were fragmented using the QIAseq FX DNA Library it with either a 5- or 10-minute run time. Fragment sizes were highly reproducible for all samples for each run time.
9
Minimal GC bias compared to other enzymatic methods
Due to its highly sequence-independent fragmentation, QIAseq FX exhibits minimal GC bias, which is comparable to mechanical shearing. 100 ng genomic DNA was used as the input in comparative library preparation and sequencing. The QIAseq FX DNA Library Kit and the leading mechanical shearing method (Supplier C) produced similar and consistent coverage across a wide range of GC contents. An all-enzymatic protocol from Supplier N yielded much higher bias toward high % GC. 1 ng genomic DNA was used as the input in a similar experiment. Again, QIAseq FX and mechanical shearing provided similar and consistent coverage, outperforming other methods.

Other supplier methods: Supplier C: mechanical shearing combined with a standard library prep; Supplier N: fragmentase; Supplier I: tagmentation.
9
Workflow
Streamlined three-step workflow. Go from purified gDNA to sequencer-ready libraries in just 2.5 hours with the QIAseq FX DNA Library Kit.
Performance
Fast and efficient enzymatic library conversion 

The new QIAseq FX DNA Library Kit takes you from 20 pg – 1 μg genomic DNA to sequencer-ready, amplified libraries in just 2.5 hours. It’s faster and easier to automate than mechanical shearing but still generates the high-quality libraries you need for whole genome sequencing of any organism (see figure: Workflow). The workflow reliably generates reproducible DNA fragments of customizable sizes. (see figures: Customizable fragment sizes and High Reproducibility

 

Low GC bias for superior library quality 

The QIAseq FX DNA Library Kit performs library preparations with minimal bias by using sequence-independent enzymes for fragmentation – delivering results comparable to mechanical shearing. (see figure: Minimal GC bias compared to other enzymatic methods)

 

Superior coverage distribution and lower duplication rate

QIAseq FX technology with its minimal sequence bias ensures that the majority of genomic targets have very similar total coverage depth. This reduces the need for additional sequencing to bring low-coverage targets up to an interpretable coverage range, saving time and resources. Sequencing libraries generated by the QIAseq FX method have high complexity and low duplicate rates, overcoming the shortcoming commonly associated with other enzymatic fragmentation methods. (see figures: Superior coverage distribution and Lower duplication rate)

 

PCR-free libraries from as little as 100 ng input

Fully functional dual bar-coded adapters and optional high-fidelity library amplification reagents enable the use of QIAseq FX fragmentation and adapter ligation chemistries to generate PCR-free libraries in under two hours total workflow time. Without additional PCR library amplification, the QIAseq FX DNA Library Kit can consistently generate the higher than 2 nM PCR-free library concentration needed for sequencing on an Illumina MiSeq or NextSeq 500 – from as little as 100 ng input DNA. (see figure: No significant differences between coverage of high or low GC genomic regions)

Principle

QIAGEN’s QIAseq FX technology incorporates enzymatic DNA fragmentation into a streamlined, optimized protocol that combines fragmentation and adapter ligation in one reaction, saving time and preventing errors. The QIAseq FX kit contains a novel nuclease formulation that digests dsDNA in a random fashion without sequence preference, generating sequencing libraries with minimal bias. The fragment size is tunable simply by changing incubation time of the dsDNA with the nuclease, enabling different sequencing applications. Optimized enzyme and buffer compositions ensure high sequencing library yield. Streamlined library construction protocols also enable straightforward automation of library prep on different liquid-handling platforms.

The QIAGEN QIAseq FX DNA Library Kit provides a fast, fully enzymatic procedure, from DNA fragmentation to NGS library, with no cleanup steps until after adapters have been ligated to the sample DNA.

Procedure
Overview

The QIAseq FX DNA Library Kit consists of three, easy-to-follow steps starting from genomic DNA and ending with sequencer-ready NGS libraries. Beginning with combined DNA fragmentation and end modification, sample fragments are prepared allowing for the binding of dual bar-coded adapters. For samples that are less than 100 ng of input DNA or if large amounts of library DNA are required in later applications, an optional DNA amplification step can be performed with reagents conveniently provided in this kit.

 
DNA fragmentation and adapter ligation

Samples consisting of longer DNA fragments, such as genomic DNA or amplicons from long-range PCR, are first enzymatically sheared into smaller fragments. The median fragment size is dependent on the applications and sequencing read length, and can be adjusted by varying the DNA fragmentation reaction conditions. The fragmented DNA is directly end-repaired, and an 'A’ is added to the 3’ ends during the FX reaction ­– making the DNA fragments ready for adapter ligation. Following this step, platform-specific adapters are ligated to both ends of the DNA fragments. These adapters contain sequences essential for binding dual bar-coded libraries to a flow cell for sequencing, allowing for PCR amplification of adapter-ligated fragments and for binding of standard Illumina sequencing primers.

 
DNA amplification

To ensure maximum yields from limited amounts of starting material, a high-fidelity amplification step can be performed using the reagents included in the QIAseq FX DNA Library Kit. The proprietary HiFi PCR Master Mix can evenly amplify DNA regions with vastly different GC contents, minimizing sequencing bias caused by PCR. 

 
Library construction

Dual bar-coded, plate-format adapters are included with the QIAseq FX DNA Library Kit. Each well contains a single-use adapter consisting of a unique combination of two eight-nucleotide identification bar codes. By combining one D5 bar code and one D7 bar code in each ready-to-use adapter, QIAseq FX kits support up to 24-plex or 96-plex pooling prior to sequencing.  

 
Cleanup and removal of adapter-dimers

Following library construction, the reaction cleanup and removal of adapter dimers can be achieved by using Agencourt® AMPure® XP Beads, enabling easy automation on various high throughput automation platforms.

Applications
QIAseq FX DNA Library Kit generates high-quality whole genome libraries for use on any Illumina platform in just 2.5 hours from purified genomic DNA to sequencer-ready libraries. Libraries are compatible with hybrid capture-based whole exome sequencing (WES) and targeted sequencing.

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