Overview
Illumina DNA PCR-Free Prep offers a rapid and flexible workflow for preparing libraries for use in sensitive whole-genome sequencing applications, such as human whole-genome sequencing (WGS), de novo assembly of microbial genomes, and tumor–normal variant calling.
Reduces cost by eliminating pre- and post-library quantification steps
Provides highly uniform coverage across repetitive or uneven genome regions
Delivers fast, automation-compatible workflow in 90 min
Simplify lab operations
The Illumina DNA PCR-Free Prep workflow supports a broad DNA input range, multiple sample types, and both small and large genomes. The workflow includes DNA extraction from blood, saliva, or dried blood spots.
Obtain reliable results
On-bead tagmentation chemistry combined with PCR-free library preparation eliminates PCR-induced bias and diminishes opportunities for error, providing superior and even coverage across high-GC or -AT regions. Learn more about on-bead tagmentation.
Access flexible throughput
The Illumina DNA/RNA UD Indexes Sets offer up to 384 unique dual indexes, enabling accurate assignment of reads and efficient use of the flow cell.
Illumina DNA Prep product line
Find fast, optimized sequencing library preparation solutions for use in a wide range of applications.
Illumina DNA PCR-Free Prep
An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
Illumina DNA Prep
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Illumina DNA Prep with Enrichment
A complete targeted resequencing solution for a wide range of applications, with fast integrated workflow and options for custom and fixed enrichment panels.
Applications
The Illumina DNA PCR-Free Prep delivers PCR-free sequencing-ready libraries for sensitive applications such as tumor–normal variant identification or human whole-genome sequencing (WGS) in approximately 1.5 hours.
Example workflow
Illumina DNA PCR-Free Prep
MiSeq System
NextSeq 550 System
NextSeq 1000 and 2000 Systems
NovaSeq 6000 System
NovaSeq X Series
DRAGEN secondary analysis
DRAGEN Germline
DRAGEN Somatic
DRAGEN PopGen
Emedgene
Project recommendations
Instrument: Recommended number of samples
NovaSeq 6000 System: S1 flow cell: 3 (based on 607M reads, 40× coverage, or > 160 Gb of total data passing filter) S2 flow cell: 6 (based on 663M reads, 40× coverage, or > 160 Gb of total data passing filter) S4 flow cell: 16 (based on 669M reads, 40× coverage, or > 160 Gb of total data passing filter)
S1 flow cell: 3 (based on 607M reads, 40× coverage, or > 160 Gb of total data passing filter)
S2 flow cell: 6 (based on 663M reads, 40× coverage, or > 160 Gb of total data passing filter)
S4 flow cell: 16 (based on 669M reads, 40× coverage, or > 160 Gb of total data passing filter)
2 × 150 bp
Related applications and methods
Human whole-genome sequencing
Human WGS provides an unbiased view of the entire human genome and the genetic variants that encode human traits and disease.
Tumor-normal sequencing
Tumor-normal studies involve comparing tumor and matched normal samples to discover somatic variants that act as cancer driver mutations.
Population genomics
Population genomics programs integrate large-scale genomic and clinical research data into a learning health system, driving health care innovation.
Figures
Illumina DNA PCR-Free Prep chemistry
A unique combination of on-bead tagmentation with a PCR-free workflow in a single, rapid reaction.
Comparison of read coverage across GC-rich regions
The Illumina DNA PCR-Free Prep kit provides superior read coverage across the GC-rich promoter region of the human RNPEPL1 gene, as compared to TruSeq DNA PCR-Free and TruSeq DNA Nano Library Prep Kits.
Illumina DNA PCR-Free Prep coverage uniformity
The Illumina DNA PCR-Free Prep provides uniform coverage across a range of GC content in the human genome.
Illumina DNA PCR-Free Prep performance across a range of DNA inputs
Illumina DNA PCR-Free Prep libraries prepared from a range of DNA inputs demonstrate (A) passing quality specifications for all DNA inputs and (B) equivalent callability performance.
Increased insert size with additional bead purification
An additional round of bead purification results in increased insert sizes (gray and yellow lines), as compared to the unmodified protocol (blue and orange lines).
Resources
Illumina DNA PCR-Free Prep, Tagmentation: Introduction
This webinar discusses the library preparation workflow and sequencing considerations and provides tips for successful next-generation sequencing projects.
Illumina® DNA PCR-Free Prep, Tagmentation (24 Samples)
20041794
Includes reagents and Illumina Purification Beads for preparing 24 libraries. Purchase index adapters separately. View less
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Illumina® DNA PCR-Free Prep, Tagmentation (96 Samples)
20041795
Includes reagents and Illumina Purification Beads for preparing 96 libraries. Purchase index adapters separately. View less
Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)
20091654
Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately. View less
Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)
20091656
Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately. View less
Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)
20091658
Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately. View less
Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)
20091660
Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately. View less
Illumina DNA PCR-Free Prep-Customer Site
20046010
1-day customer-site training for Illumina DNA PCR-Free Prep. Hands-on training includes quantification of DNA input as well as best practices, troubleshooting tips, and training on Illumina-supported analysis tools specific to the application workflow. View less
Illumina® DNA PCR-Free Sequencing and Indexing Primer
20041797
Includes two, 7.5-ml tubes of VP10 custom read 1 primer and two, 7.5-ml tubes of VP14 custom index 2 primer for use on the iSeq 100, MiniSeq, NextSeq 500/550, NextSeq 1000/2000, and HiSeq 3000/4000 Systems. View less
Illumina® Lysis Kit
20042221
Includes one lysis kit to process blood samples with the Illumina DNA PCR-Free Prep. Purchase library prep and index adapters separately. View less
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What is PCR-free library prep?
PCR-free library preparation is the construction of a DNA library without the use of PCR amplification. Illumina DNA PCR-Free chemistry eliminates PCR-induced bias and provides highly accurate sequence information for sensitive applications.
How does Illumina DNA PCR-Free Prep work?
PCR-free library preparation uses a bead-linked transposome complex to tag genomic DNA by fragmenting and adding adapter tag sequences in a single and rapid reaction step. The single reaction step is called on-bead tagmentation. After the bead-linked transposomes are saturated with DNA, no additional tagmentation can occur, delivering consistent library yield and insert sizes.
Learn more about on-bead tagmentation
What is PCR-free sequencing?
PCR-free sequencing eliminates PCR amplification steps, significantly reducing typical PCR-induced bias and uneven amplification.
Why use Illumina DNA PCR-Free Prep?
Illumina DNA PCR-Free Prep workflow uses on-bead tagmentation, allowing for consistent insert sizes, uniform coverage, and enhanced performance, regardless of DNA input amount or genome size in a single, rapid reaction. On-bead tagmentation eliminates the need for PCR amplification steps, minimizing biased base composition and opportunities for error, making this kit ideal for sensitive sequencing applications.
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