An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
Assay time
Hands-on time
Input quantity
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.
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.
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.
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.
Find fast, optimized sequencing library preparation solutions for use in a wide range of applications.
An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
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.
| Assay time | ~1.5 hr |
|---|---|
| Automation capability | Liquid handling robots |
| Automation details | Explore available automation methods |
| Description | Prepare sequencing libraries for sensitive applications using a unique combination of on-bead tagmentation with PCR-free chemistry which simultaneously eliminates PCR-induced bias and reduces total library prep time to 90 minutes. |
| Hands-on time | ~45 min |
| Input quantity | 25 ng to 300 ng |
| Instruments | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, NextSeq 550Dx in Research Mode, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System |
| Mechanism of action | Bead-linked transposome |
| Method | De novo sequencing, Whole-genome sequencing |
| Multiplexing | Up to 384-plex |
| Nucleic acid type | DNA |
| Specialized sample types | Blood, Not FFPE-compatible, Low-input samples, Saliva, Not FFPE-compatible |
| Species category | Any species, Human |
| Target insert size | 450 bp +/- 75 bp |
| Technology | Sequencing |
| Variant class | Short tandem repeats (STRs), Single nucleotide polymorphisms (SNPs), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) |
| Automation capability | Liquid handling robots |
|---|---|
| Instruments | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, NextSeq 550Dx in Research Mode, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System |
| Method | De novo sequencing, Whole-genome sequencing |
| Nucleic acid type | DNA |
| Specialized sample types | Blood, Not FFPE-compatible, Low-input samples, Saliva |
| Species category | Any species, Human |
| Technology | Sequencing |
| Variant class | Short tandem repeats (STRs), Single nucleotide polymorphisms (SNPs), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) |
Purchase the Illumina DNA PCR-Free Sequencing and Indexing Primer (cat. no. 20041797) for all instruments except the NovaSeq 6000 System.
Index adapters are optional but recommended for multiplexing. Choose the number of indexes needed to match your sample throughput. We recommend ordering the Illumina DNA/RNA UD Indexes Sets A-D (20091654, 20091656, 20091658, 20091660). The IDT for Illumina DNA/RNA UD Indexes Sets A-D (20027213, 20027214,20042666, 20042667) are being discontinued.
Learn more about multiplexing.
The Illumina Lysis Kit is required only for processing blood samples.
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.
Illumina DNA PCR-Free Prep
| Instrument | Recommended number of samples | Read length |
|---|---|---|
| NovaSeq 6000 System | S1: 3 (based on 607M reads, 40× coverage, or > 160 Gb of total data passing filter) S2: 6 (based on 663M reads, 40× coverage, or > 160 Gb of total data passing filter) S4: 16 (based on 669M reads, 40× coverage, or > 160 Gb of total data passing filter) |
2 × 150 bp |
Human whole-genome sequencing provides the most detailed view into the complex genetic variants that make us unique.
Both high- and low-throughput walk-away automation methods are available through our automation partners to reduce hands-on time and minimize errors.
Tumor-normal studies involve comparing tumor and matched normal samples to discover somatic variants that act as cancer driver mutations.
| Illumina DNA PCR-Free Prep | Illumina DNA Prep | TruSeq DNA PCR-Free | TruSeq DNA Nano | |
|---|---|---|---|---|
| Assay time | ~1.5 hr | ~3-4 hr (from DNA extraction to normalized library) | 5 hr total assay time | ~6 hr total assay time |
| Automation capability | Liquid handling robots | Liquid handling robots | Liquid handling robots | Liquid handling robots |
| Automation details | Explore available automation methods | Explore available automation methods | Explore available automation methods | Explore available automation methods |
| Description | Prepare sequencing libraries for sensitive applications using a unique combination of on-bead tagmentation with PCR-free chemistry which simultaneously eliminates PCR-induced bias and reduces total library prep time to 90 minutes. | A fast, flexible library prep workflow that accommodates an assortment of sample types and DNA input amounts, allowing access to a wide range of applications, from human to microbial whole-genome sequencing and more. | A simple, all-inclusive PCR-free prep for whole-genome sequencing studies with the ability to sequence through challenging regions of the genome. | A low-input research method that delivers high genome coverage quality and reduced bias. |
| Hands-on time | ~45 min | 1-1.5 hr | 4 hr | ~4 hr |
| Input quantity | 25 ng to 300 ng | 1-500 ng DNA for small genomes (e.g. microbial), or 100-500 ng DNA for large genomes (e.g. human). (For blood and saliva, see the reference guide). | 1 ug DNA | 100 ng genomic DNA |
| Instruments | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, NextSeq 550Dx in Research Mode, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System | MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System | MiSeq System, NextSeq 550 System, NextSeq 2000 System, MiSeqDx in Research Mode, MiniSeq System, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System |
| Mechanism of action | Bead-linked transposome | Bead-linked transposome | Mechanical DNA fragmentation and adapter ligation. Workflow is PCR-free and gel-free. | Mechanical DNA fragmentation and adapter ligation. Workflow uses reduced-bias PCR and is gel-free. |
| Method | De novo sequencing, Whole-genome sequencing | Amplicon sequencing, De novo sequencing, Whole-genome sequencing, Shotgun sequencing | Genotyping by sequencing, Whole-genome sequencing, Shotgun sequencing | Genotyping by sequencing, Whole-genome sequencing, Shotgun sequencing |
| Multiplexing | Up to 384-plex | Up to 384 unique dual (UD) combinations and 96 combinatorial dual (CD) combinations | Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations | Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations |
| Nucleic acid type | DNA | DNA | DNA | DNA |
| Specialized sample types | Blood, Not FFPE-compatible, Low-input samples, Saliva, Not FFPE-compatible | Blood, Not FFPE-compatible, Saliva | Not FFPE-compatible | Not FFPE-compatible, Low-input samples |
| Species category | Any species, Human | Drosophila, Any species, Mammalian, Mouse, Yeast, Zebrafish, Human, Rat, Plant, Virus, Nematode, Bacteria | Other, Mammalian, Mouse, Human, Rat, Plant | Other, Mammalian, Mouse, Human, Rat, Plant |
| Target insert size | 450 bp +/- 75 bp | ~350 bp | 350 bp or 550 bp | 350 bp or 550 bp |
| Technology | Sequencing | Sequencing | Sequencing | Sequencing |
| Variant class | Short tandem repeats (STRs), Single nucleotide polymorphisms (SNPs), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) | Single nucleotide polymorphisms (SNPs), Gene fusions, Loss of heterozygosity (LOH), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) | Single nucleotide polymorphisms (SNPs), Gene fusions, Loss of heterozygosity (LOH), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) | Single nucleotide polymorphisms (SNPs), Gene fusions, Loss of heterozygosity (LOH), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs) |
Library Prep and Array Kit Selector
Find the right sequencing library preparation kit or microarray for your needs. Filter by method, species, and more. Compare, share, and order kits.
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.
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.
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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.
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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.
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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.
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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.
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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.
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IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)
20027213
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)
20042666
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)
20042667
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)
20027214
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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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.
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.
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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.
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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.
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
PCR-free sequencing eliminates PCR amplification steps, significantly reducing typical PCR-induced bias and uneven amplification.
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.
Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
A high-performance, fast, and reliable human whole-exome sequencing solution that includes a comprehensive, up-to-date exome enrichment panel.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Reagent kits for the NovaSeq 6000 System consisting of ready-to-use pre-filled reagent cartridges and flow cells.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI) from FFPE tissue, with added scalability.
Enable CGP with a pan-cancer panel capable of detecting key IO gene signatures (TMB, MSI) plus all main variant classes from ctDNA in blood plasma.
NovaSeq 6000 Xp Workflow delivers the flexibility of independent lane loading and high library multiplexing per flow cell, maximizing sample throughput on a single run.
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