Illumina DNA Prep Training
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Illumina DNA Prep offers flexibility for many whole-genome sequencing applications.
Learn more about the technology
Illumina DNA Prep uses a fast, user-friendly workflow. On-bead tagmentation chemistry reduces total library prep time to ~3.5 hours, from DNA extraction to library normalization.
The Illumina DNA Prep workflow supports a broad DNA input range (1–500 ng), multiple sample types, and both small and large genomes. The workflow includes DNA extraction from blood, saliva, or dried blood spots*or bacterial colonies*.
Gain the flexibility to sequence human or other large, complex genomes as well as amplicons or microbial species, all with a single kit.
While accommodating various study requirements, the Illumina DNA Prep 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, resulting in highly reproducible sequencing data.
The IDT for Illumina - DNA/RNA UD Indexes Sets A, B, C, and D offer up to 384 unique dual indexes, enabling accurate assignment of reads and efficient use of the flow cell. (Sets A and B are available now. Sets C and D are coming soon.) These unique dual index codes use 10 base pair codes. This change in base pair index codes require adjustments to the sequencing run setup.
Nextera DNA CD Indexes support up to 96-sample combinatorial dual indexing. The 24 CD Indexes are supplied in a tube format, and 96 in a plate format.
For whole-genome sequencing, Illumina DNA Prep is the recommended replacement for the Nextera DNA Library Prep Kit, which has been discontinued. If you were using Nextera DNA (Cat. No. FC-121-1030) or stand-alone components (Cat. Nos. 15027865 and 15027866) for ATAC-Seq** or other custom applications, the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit is our suggested alternative.
Prepare libraries for Illumina sequencing in less than a day. Illumina Qualified Methods are available on a range of automation platforms through our partners.
*Demonstrated protocols available.
**Customer-reported application
Discover the power that Illumina library prep tagmentation technology can bring to your lab through this interactive experience. Our library prep solutions offer whole-genome sequencing across various applications, flexibility across Illumina sequencers, and integrated sample input for blood and saliva without quantification.
View Infographic
| Instrument | Recommended Number of Samples | Read Length |
|---|---|---|
| NextSeq 550 System | 1 sample per run (high output; based on 30× coverage of a human genome) | Up to 2 × 150 bp |
| NovaSeq 6000 System | 2–10 samples per run (dual flow cell; based on 30× coverage of a human genome) | Up to 2 × 125 bp (rapid run) Up to 2 × 150 bp (high output) |
| Illumina DNA Prep | TruSeq DNA PCR-Free | TruSeq DNA Nano | |
|---|---|---|---|
| Assay Time | ~3-4 hours (from DNA extraction to normalized library) | 5 hours total assay time | ~6 hours total assay time |
| Automation Capability | Liquid Handling Robots | Liquid Handling Robots | Liquid Handling Robots |
| Description | A fast, flexible workflow for a wide range of research applications and sample types, 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 | 1-1.5 hours | 4 hours | ~4 hours |
| Input Quantity | 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). | 1 ug DNA | 100 ng genomic DNA |
| 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. |
| Method | Amplicon Sequencing, De Novo Sequencing, Shotgun Sequencing, Whole-Genome Sequencing | Genotyping by Sequencing, Shotgun Sequencing, Whole-Genome Sequencing | Genotyping by Sequencing, Shotgun Sequencing, Whole-Genome Sequencing |
| Multiplexing | 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 (available soon) | Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations (available soon) |
| Specialized Sample Types | Blood, Not FFPE-Validated, Saliva | Not FFPE-Compatible | Low-Input Samples, Not FFPE-Compatible |
| Species Category | Any Species, Bacteria, Drosophila, Human, Mammalian, Mouse, Nematode, Plant, Rat, Virus, Yeast, Zebrafish | Human, Mammalian, Mouse, Other, Plant, Rat | Human, Mammalian, Mouse, Other, Plant, Rat |
| Species Details | Compatible with any species | Compatible with most large DNA genomes. | Compatible with most large DNA genomes. |
| Target Insert Size | ~350bp | 350 bp or 550 bp | 350 bp or 550 bp |
(A) Bead-linked transposomes mediate the simultaneous fragmentation of gDNA and the addition of Illumina sequencing primers. (B) Reduced-cycle PCR amplification amplifies sequencing ready DNA fragments and adds indexes and adapters. (C) Sequencing-ready fragments are washed and pooled.
Application Note | PDF 3 MB
An automated Nextera DNA Flex library preparation workflow for high-throughput metagenomics
Application Note | PDF < 1 MB
Nextera Crude Lysate Protocol for Metagenomic Whole-Genome Sequencing Studies
Application Note | PDF < 1 MB
Direct Bacterial Colony Sequencing with the Nextera™ DNA Flex Library Preparation Kit
Application Note | PDF 1 MB
Fast, Flexible, and Self-Normalizing Library Prep with Nextera Flex Chemistry
Application Note | HTML
Nextera DNA Flex Library Preparation for Soil Shotgun Metagenomics Analysis
Application Note | HTML
Illumina library preparation solutions
Brochure | PDF 2 MB
Data Sheet | PDF | 6 versions
Trim Adapters for Nextera DNA Flex in Local Run Manager for MiniSeq Documentation
Illumina DNA Prep Checklist Documentation
Illumina DNA Prep Support Documentation
Illumina DNA Prep Reference Guide Documentation
Illumina DNA Prep Consumables & Equipment List Documentation
Nextera DNA Flex Dried Blood Spot Protocol Guide Documentation
Index Adapters Pooling Guide Documentation
Custom Protocol Selector
Generates customized, end-to-end instructions
Focused sequencing panel to assess 15 genes that are commonly mutated in solid tumors in a single assay, with a simple, rapid workflow.
This kit provides a low-cost exome sequencing solution that delivers exceptional target coverage over a broad range of read depths.
Kits include SBS reagents, clustering reagents, and patterned flow cells for increased cluster density and simplified image analysis, compared to non-patterned flow cells.
MiSeq sequencing reagents in pre-filled, ready-to-use cartridges. Micro and nano formats are available for low output applications.
This kit enables cluster generation for subsequent sequencing on the HiSeq 3000 and HiSeq 4000 Systems.
Prepare sequencing libraries for small genomes, PCR amplicons, plasmids, or cDNA in as little as 90 minutes, with a low DNA input requirement.
