Library preparation for the major next generation sequencing (NGS) platforms requires the ligation of specific adaptor oligos to fragments of the DNA to be sequenced. First, DNA is fragmented to the optimal length determined by the downstream platform. Because DNA fragmentation does not result in homogeneous, blunt-ended fragments, end repair is needed to ensure that each molecule is free of overhangs, and contains 5′ phosphate and 3′ hydroxyl groups. Libraries to be used in blunt-ended adaptor ligation, including Ion Torrent™ library construction, can be used directly in the ligation step. For Illumina® libraries, incorporation of a non-templated deoxyadenosine 5′-monophosphate (dAMP) onto the 3′ end of blunted DNA fragments, a process known as dA-tailing, is necessary. dA-tails prevent concatamer formation during downstream ligation steps, and enable DNA fragments to be ligated to adaptors with complementary dT-overhangs. The desired adaptor-ligated DNA size can be achieved via bead-based size selection before optional PCR amplification. New England Biolabs supplies reagents for DNA library preparation for the leading sequencing platforms. For more information, choose the DNA Library Construction Workflow tab below.
Ion Torrent™ and SOLiD™ 4 are trademarks owned by Life Technologies, Inc.
Illumina® is a registered trademark of Illumina, Inc.
- Control Reaction Protocol for PreCR Repair Mix
- Data Analysis - NEBNext Library Quant Kit (E7630)
- Double Digest Protocol with Standard Restriction Enzymes
- Expected Results - NEBNext Library Quant Kit (E7630)
- Experimental Considerations - NEBNext Library Quant Kit (E7630)
- Guidelines for Running Samples on the Illumina MiSeq (E7000)
- Guidelines for Running Samples on the Illumina MiSeq (E6627)
- Guidelines for Setting up PCR Reactions (E6627X only)
- Guidelines for Setting Up PCR Reactions (E7000X only)
- Index Pooling Guidelines - 96 Single Index Kit (E6609)
- Ligation Protocol with T4 DNA Ligase (M0202)
- Loop-mediated Isothermal Amplification (LAMP)
- NEBNext FFPE DNA Repair Mix (M6630) - Protocol for use with Other User-supplied Library Construction Reagents
- NEBNext Library Quant Kit Protocol - NEBNext Library Quant Kit (E7630)
- NEBNext Library Quant Kit Quick Protocol (E7630)
- Optimizing Restriction Endonuclease Reactions
- PCR Using NEBNext® High-Fidelity 2X PCR Master Mix (M0541)
- Protocol for a PCR reaction using NEBNext® Q5® Hot Start HiFi PCR Master Mix (M0543)
- Protocol for a PCR reaction using NEBNext® Ultra™ II Q5® Master Mix (M0544)
- Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using DNA Polymerase I, Large (Klenow) Fragment (M0210)
- Protocol for blunting ends by 3’ overhang removal and 3’ recessed (5’ overhang) end fill-in using T4 DNA Polymerase (M0203)
- Protocol for Cre Recombinase (M0298)
- Protocol for Digestion Prior to droplet digital PCR (ddPCR)
- Protocol for Direct Digestion of gDNA during droplet digital PCR (ddPCR)
- Protocol for NEBNext Direct BRCA1/BRCA2 Panel (E6627)
- Protocol for NEBNext Direct® Cancer HotSpot Panel (NEB #E7000)
- Protocol for use with NEBNext FFPE DNA Repair Mix (M6630) and NEBNext DNA Library Prep Master Mix Set for Illumina (E6040)
- Protocol for use with NEBNext Ultra DNA Library Prep Kit for Illumina (E7370)
- Protocol for use with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, E7103)
- Protocol for use with NEBNext® Ultra™ II End Repair/dA-Tailing Module (E7546)
- Quick Ligation Protocol (M2200)
- Sequential Reaction Protocol for PreCR Repair Mix
- Setting up the PCR Reactions < 96 Samples and 96 Samples - 96 Single Index Kit (E6609)
- Standard Reaction Protocol for PreCR Repair Mix
- Transformation Protocol
Enzymatic Methyl-seq: The Next Generation of Methylome Analysis
Improving Enzymatic DNA Fragmentation for Next Generation Sequencing Library Construction
Among the available options for DNA fragmentation, enzymatic fragmentation is demonstrably gentler on the sample, yielding less damage at any scale. The new NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® includes a single step for enzymatic fragmentation, end repair, and dA tailing.
The Quantitation Question: How does accurate library quantitation influence sequencing?
The determination of the number of sequencing-ready molecules present after library preparation is an important step in the next generation sequencing (NGS) workflow and has a strong influence on the success of both a sequencing run and a sequencing-based experiment.
- A Robust, Streamlined, Enzyme-based DNA Library Preparation Method Amenable to a Wide Range of DNA Inputs (2019)
- A Single-tube, Low Input Protocol for Long Read Sequencing (2019)
- EM-seq™ Enables Accurate and Precise Methylome Analysis of Challenging DNA Samples (2019)
- NEBNext Direct® Custom Ready Panels Overcome Challenges Associated with Targeted Re-sequencing (2019)
- NEBNext® Ultra™II FS DNA: A Robust Enzyme-based DNA Library Preparation Method Compatible with Plant and Animal Samples (2019)
While NEB develops and validates its products for various applications, the use of this product may require the buyer to obtain additional third party intellectual property rights for certain applications.
For more information about commercial rights, please contact NEB's Global Business Development team at [email protected].
This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.
This video walks you through DNA Library Preparation using the NEBNext Ultra II DNA Library Prep Kit. The video also includes tips for optimization as well as safe stopping points.
In this webinar, Laurence Etwiller and Jennifer Ong discuss their recent publications, and how library preparation affects sequencing accuracy and variant calling. View full Q & A summary.
Get a quick overview of NGS library preparation from an NEB scientist.
This video will help you decide if you need to do a size selection or a simple clean-up for the NEBNext Ultra DNA or RNA.