We recommend ordering the new 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 obsolete and the last order date is January 30, 2025, as announced in PON2023-1440.
Illumina DNA PCR-Free Prep
A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.
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Illumina DNA PCR-Free Prep Training
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Product Highlights
Illumina DNA PCR-Free Library Prep offers flexibility for many whole-genome sequencing applications.
- Fast, automatable workflow, with ~1.5 hours total time
- Flexibility to accommodate variations in sample type, DNA input amount, and application
- Optimized library prep performance, generating reliable results
Save Time and Resources
The Illumina DNA PCR-Free Library Prep Kit uses a fast, user-friendly workflow. On-Bead Tagmentation chemistry reduces total library prep time to ~1.5 hours, from DNA extraction to library normalization.
Simplify Lab Operations
The Illumina DNA PCR-Free workflow supports a broad DNA input range (25 ng to 300 ng), multiple sample types, and both small and large genomes. The workflow includes DNA extraction from blood, saliva, or dried blood spots.
You can use liquid-handling robots to automate workflows for minimal touch points and significant time savings.
Obtain Reliable Results
While accommodating various study requirements, the Illumina DNA PCR-Free workflow delivers consistent insert sizes, uniform coverage, and optimized performance, regardless of DNA input amount or genome size. The bead-based technology minimizes bias and opportunities for error, delivering accurate base calling and variant identification for a broad range of DNA input amounts.
Access Flexible Throughput Options
The Illumina - DNA/RNA UD Indexes Sets A, B, C, and D Indexes offer up to 384 unique dual indexing that enables accurate assignment of reads and efficient use of the flow cell. These unique dual index codes use 10 base pair codes. This change in base pair index codes require adjustments to the sequencing run setup.
Fast, Automation-friendly Workflow
Prepare libraries for Illumina sequencing in less than a day. Illumina Qualified Methods are available on a range of automation platforms through our partners.
Frequently Purchased Together
Specifications
Product Comparison
| Illumina DNA PCR-Free Prep | TruSeq DNA PCR-Free | TruSeq DNA Nano | Illumina DNA Prep | |
|---|---|---|---|---|
| Assay Time | ~1.5 hours | 5 hours total assay time | ~6 hours total assay time | ~3-4 hours (from DNA extraction to normalized library) |
| Automation Capability | Liquid Handling Robots | Liquid Handling Robots | Liquid Handling Robots | Liquid Handling Robots |
| Input Quantity | 25 ng to 300 ng | 1 ug DNA | 100 ng genomic DNA | Small genomes (e.g. microbial): 1-500 ng DNA. Large genomes (e.g. human): 100-500 ng DNA. (For blood and saliva, see the reference guide). |
| Mechanism of Action | 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. | Bead-linked transposome |
| Method | De Novo Sequencing, Whole-Genome Sequencing | Genotyping by Sequencing, Shotgun Sequencing, Whole-Genome Sequencing | Genotyping by Sequencing, Shotgun Sequencing, Whole-Genome Sequencing | Amplicon Sequencing, De Novo Sequencing, Shotgun Sequencing, Whole-Genome Sequencing |
| Multiplexing | Up to 384-plex | Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations (available soon) | Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations (available soon) | Up to 384 unique dual (UD) combinations and 96 combinatorial dual (CD) combinations |
| Nucleic Acid Type | DNA | DNA | DNA | DNA |
| Specialized Sample Types | Blood, Low-Input Samples, Not FFPE-Compatible, Saliva | Not FFPE-Compatible | Low-Input Samples, Not FFPE-Compatible | Blood, Not FFPE-Validated, Saliva |
Case Studies
Optimizing WGS workflows
Dr. Pietro Cattaneo and Dr. Cédric Howald from the Health 2030 Genome Center discuss their experience incorporating IGA and Illumina DNA PCR-Free Prep in their workflows and how deploying these solutions has enabled them to meet the demands of their large-scale WGS projects.
Read InterviewIllumina DNA PCR-Free chemistry
An efficient solution for preparing and indexing sample libraries.
Illumina DNA PCR-Free coverage uniformity
An efficient solution for preparing and indexing sample libraries.
Comparison of read coverage across GC-rich regions
The Illumina DNA PCR-Free Library 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. Read maps were visualized with the Integrative Genomics Viewer (IGV) App, available in BaseSpace Sequence Hub.
Illumina DNA PCR-Free performance across a range of DNA inputs
Illumina DNA PCR-Free libraries prepared from a range of DNA inputs demonstrate (A) passing quality specifications for all DNA inputs and (B) equivalent callability performance. Q30 score = an inferred base call accuracy of 99.9%, autosome callability = the percentage of non-N reference positions in autosomal chromosomes with a passing genotype call, exon callability = the percentage of non-N reference positions in exons with a passing genotype call, SNPs = single nucleotide polymorphisms, indel = insertion-deletion mutation, precision (accuracy) = calculated as the ratio of [# of True Positive Calls/(# of True Positive Calls + # of False Positive Calls)], recall (sensitivity) = calculated as the ratio of [# of True Positive Calls/(# of True Positive Calls + # of False Negative Calls)]. Note: the lower limit sample input specifications for Illumina DNA PCR-Free have not been finalized.
Product Literature
Microbial whole-genome sequencing with Illumina DNA PCR-Free Prep, Tagmentation
Application Note | PDF < 1 MB
High-performance whole-genome sequencing with Illumina DNA PCR-Free Prep, Tagmentation
Application Note | PDF < 1 MB
Tunable insert sizes with Illumina DNA PCR-Free Prep, Tagmentation
Application Note | PDF < 1 MB
Illumina library preparation solutions
Brochure | PDF 2 MB
Application Note | PDF | 5 versions
Optimal loading concentrations for Illumina DNA PCR-Free libraries
Technical Note | PDF < 1 MB
Balancing sample coverage for whole-genome sequencing
Technical Note | PDF < 1 MB
Data Sheet | PDF | 5 versions
Illumina DNA PCR-Free Prep index correction
product_file | CSV < 1 MB
Manuals and Support Information
Illumina Adapter Sequences Documentation
NovaSeq Series Custom Primers Guide Documentation
Custom Protocol Selector
Generates customized, end-to-end instructions
All Illumina DNA RNA UD Indexes Support All Illumina DNA PCR-Free Support
Illumina Stranded Total RNA Prep with Ribo-Zero Plus or Ribo-Zero Plus Microbiome
Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with exceptional study flexibility.
NovaSeq 6000 Reagent Kits
Reagent kits for the NovaSeq 6000 system provide ready-to-use cartridge-based reagents for cluster generation and SBS.
NovaSeq Xp Workflow
The NovaSeq Xp workflow enables labs to load libraries directly into each lane of a NovaSeq 6000 System flow cell, without additional instrumentation.
Illumina RNA Prep with Enrichment
Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
TruSight Cardio Sequencing Panel
This kit provides researchers with a comprehensive, cost-effective solution for identifying causal variants implicated in inherited cardiac conditions (ICCs).
TruSight Oncology 500 High-Throughput
Enabling comprehensive genomic profiling from FFPE samples, with added flexibility to batch up to 192 samples per flow cell.