Overview
Illumina DNA Prep, previously known as Nextera DNA Flex, offers a fast, robust, and flexible workflow for preparing normalized, sequencing-ready libraries from a wide range of DNA input types and amounts facilitating an array of applications, from human whole-genome sequencing to sequencing amplicons, plasmids, and microbial species. 1
Delivers even genome coverage and exceptional data quality
Enhances library preparation efficiency with integrated DNA extraction protocols
Provides a fast, user-friendly workflow that reduces total library prep time to ~3.5 hr
Obtain reliable results
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.
Access flexible throughput options
The Illumina DNA/RNA UD Index 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 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.
Illumina DNA PCR-Free Prep
An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
Applications
Illumina DNA Prep supports a broad DNA input range (1–500 ng) and offers high-quality libraries for sequencing samples ranging from large whole genomes to amplicons, plasmids, and microbial species, in as little as ~3.5 hours.
Example workflow
Illumina DNA Prep
MiSeq i100 Series
NextSeq 1000 & NextSeq 2000 Systems
NovaSeq 6000 System
NovaSeq X Series
DRAGEN Germline
DRAGEN Metagenomics Pipeline
DRAGEN PopGen
DRAGEN Somatic
Variant Calling Assessment Tool
BaseSpace Sequence Hub
Emedgene
Project recommendations
Instrument: Sample type and application (minimum coverage or reads/sample)
NextSeq 2000 System: Human genome (30x coverage, >120 Gb)
Bacterial isolate whole genome (30x coverage of 5 Mb genome, 150 Mb/sample): P1 - 192 samples, P2- 384 samples
Bacterial isolate whole genome (30x coverage of 5 Mb genome, 150 Mb/sample)
Shallow shotgun metagenomics (1M single reads or 2M PE reads/sample): P1 - 96 samples, P2 - 384 samples
Shallow shotgun metagenomics (1M single reads or 2M PE reads/sample)
Shotgun metagenomics (10M single reads or 20M PE reads/sample): P1 - 10 samples, P2 - 40 samples, P3 - 120 samples, P4 - 180 samples
Shotgun metagenomics (10M single reads or 20M PE reads/sample)
NovaSeq 6000 System: Human genome (30x coverage, >120 Gb)
Bacterial isolate whole genome (30x coverage of 5 Mb genome, 150 Mb/sample): SP - 384 samples
Shallow shotgun metagenomics (1M single reads or 2M PE reads/sample): SP - 384 samples
Shotgun metagenomics (10M single reads or 20M PE reads/sample): SP - 80 samples, S1- 150 samples, S2 - 384 samples
NovaSeq X System: Human genome (30x coverage, >120 Gb)
Bacterial isolate whole genome (30x coverage of 5 Mb genome, 150 Mb/sample): 1.5B - 384 samples
Shallow shotgun metagenomics (1M single reads or 2M PE reads/sample): 1.5B - 384 samples
Shotgun metagenomics (10M single reads or 20M PE reads/sample): 1.5B - 150 samples, 10B - 384 samples
Related applications and methods
Microbial whole-genome sequencing
Use microbial whole-genome sequencing to map genomes of novel organisms, finish genomes of known organisms, or compare genomes across multiple samples.
Large whole-genome sequencing
Large whole-genome sequencing informs disease research and population genomics studies and reveals disease-associated alleles.
Metagenomic sequencing
Comprehensively sample all genes in all organisms in complex samples to evaluate bacterial diversity and detect unculturable microorganisms using NGS.
Illumina bead-linked transposome chemistry
(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.
Illumina DNA Prep delivers the fastest Illumina workflow
Comparison of the total workflow time from DNA extraction to library normalization and pooling. Illumina DNA Prep produces a workflow with the least number of steps and the fastest total workflow time.
Improved coverage uniformity
(A) Illumina DNA Prep delivers uniform coverage across the genome comparable to the TruSeq DNA Nano kit. (B) Coverage is shown for microorganisms with extremely high- or low-GC content. Due to improved on-bead tagmentation library prep chemistry, Illumina DNA Prep shows more even coverage than Nextera XT.
Illumina DNA Prep: Introduction
An introductory presentation about getting started with the Illumina DNA Prep kit.
Fast, simple library prep from Illumina
Experience a fast, simple library prep and enrichment workflow from Illumina.
How Joyn Bio uses Illumina NGS
Joyn Bio, a joint venture between Ginkgo Bioworks and Bayer, uses Illumina NGS as they unite Ginkgo’s synthetic biology expertise with Bayer’s microbial and agricultural expertise to engineer microbes for agricultural solutions.
Illumina DNA Prep: A robust and self-normalizing enzymatic library prep technology
Illumina DNA Prep offers the convenience of enzymatic fragmentation and minimizes the requirement for quantitation post-library prep.
Library prep innovation pipeline at Illumina
Learn about Illumina technologies designed to offer easy-to-use, fast, and simple solutions for both DNA and RNA library preparation.
How on-bead tagmentation works
On-bead tagmentation library prep chemistry integrates DNA extraction, fragmentation, library prep, and library normalization.
Illumina DNA Prep, (M) Tagmentation (24 Samples, IPB)
20060060
Includes reagents for preparing 24 libraries. Illumina Purification Beads are included. Purchase enrichment probe panel and index adapters separately. View less
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Illumina DNA Prep, (M) Tagmentation (96 Samples, IPB)
20060059
Includes reagents for preparing 96 libraries. Illumina Purification Beads are included. Purchase enrichment probe panel and 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
Nextera™ DNA CD Indexes (96 Indexes, 96 Samples)
20018708
Includes 20 indexes, eight of i500s and 12 of i700 indexes that together provide 96 dual indexing capability sufficient for labeling 96 samples. Indexes are provided in a 96 well format. Purchase library prep and probe panels separately. View less
Illumina DNA Prep - Customer Site
20022900
A 1-day onsite training for the complete Illumina DNA Prep library preparation workflow. Participants will learn all steps of the workflow including sample input and library preparation, quality control, best practices, and troubleshooting, in addition to training on Illumina- supported sequencing and data analysis tools specific to the Illumina DNA Prep workflow. 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
Illumina Purification Beads 30 ml
20119944
Illumina Purification Beads 30 ml View less
Illumina Purification Bead, 100mL
20060057
Includes one, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately. View less
Illumina Purification Bead, 400mL
20060058
Includes four, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately. View less
Flex Lysis Reagent Kit (96 reactions)
20018706
Includes reagents for processing blood samples with the Illumina DNA Prep and Illumina DNA Prep with Enrichment. Purchase library prep, enrichment, enrichment probe panel, and index adapter reagents separately. View less
NextSeq PhiX Control Kit
FC-110-3002
DNA control for the NextSeq Illumina sequencing platform. Compatible with single and paired-end reads up to 300 bp. 10 µl of a 10 nM PhiX solution. View less
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Is the Illumina DNA Prep workflow compatible with blood and saliva samples?
Yes, Illumina has designed specific extraction protocols for both blood and saliva. The protocols can be found in the Illumina DNA Prep Reference Guide .
Which automated liquid handlers are compatible with Illumina DNA Prep?
In general, Illumina DNA Prep is designed to be compatible with most automated liquid-handling systems. Illumina automation partners are all developing methods for at least one existing automation platform.
View the library prep automation page for more information.
Can other thermal cyclers be used with the Illumina DNA Prep protocol?
Coverage of GC-rich regions can be impacted by the model, settings, and performance of the thermal cycler used. Illumina has validated the Bio-Rad DNA Engine Tetrad 2, the Bio-Rad S1000, the Bio-Rad C1000, and the MJ Research PTC-225 DNA Engine Tetrad thermal cyclers for use with Illumina DNA Prep. Other thermal cyclers may differ in their performance, which may impact genomic coverage.
Can dried blood spots be used as input in the Illumina DNA Prep workflow?
Yes, the minimum input range (1–500 ng) of Illumina DNA Prep allows the use of DNA extracted from Dried Blood Spot (DBS) cards.
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1. Bruinsma S, Burgess J, Schlingman D, et al. Bead-Linked Transposomes Enable a Normalization-Free Workflow for NGS Library Preparation. 2018;19:722. BMC Genomics. Published online 2018 Oct 1. doi: 10.1186/s12864-018-5096-9
