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NGS Sample Prep & Target Enrichment

High-quality, high-yield library preparation is a critical first step towards optimizing your next generation sequencing (NGS) workflows. The NEBNext® product line is a series of highly pure reagents for both DNA and RNA sample prep, as well as target enrichment of DNA for NGS. NEBNext kits are carefully designed and QC’d to improve yields and library diversity, using a broad range of input amounts from a wide variety of sample types. Recently, a novel enzyme-based DNA fragmentation system was added to enable streamlined DNA fragmentation, end repair, and dA tailing with a single enzyme mix; this kit, the NEBNext Ultra II FS DNA Library Prep Kit (NEB #E7805), enables reliably high-quality and high-yield library construction with as little as 100 pg of input DNA.

For those looking for a more targeted approach, NEBNext provides NEBNext Direct® for target enrichment. This unique hybridization-based technology enables high-sensitivity variant calling with a speed and precision previously only feasible using multiplex PCR-based approaches. For convenient customization, NEBNext Direct Custom Ready Panels offer ready-made, optimized baits for over 850 targets, enabling faster time to targeted results. For sequence-based target genotyping applications in plant, animal and human, the NEBNext Genotyping Solution enables pre-capture pooling of up to 96 samples for cost-effective and scalable genotyping of up to 5,000 genomic markers.

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NGS Sample Prep & Target Enrichment includes these areas of focus:

DNA Fragmentation
DNA Library Preparation
FFPE DNA Repair: NEBNext FFPE DNA Repair Mix
Illumina® Library Preparation: NEBNext® Ultra™ II RNA Library Prep; NEBNext® Ultra™ II DNA Library Prep; RNA for Illumina®; DNA for Illumina®
Ion Torrent^® DNA Library Preparation: DNA for Ion Torrent^®
NEBNext^® ARTIC products for SARS-CoV-2 sequencing
NEBNext® Automation
RNA Library Preparation

FAQs for NGS Sample Prep & Target Enrichment

Protocols for NGS Sample Prep & Target Enrichment

Application Notes for NGS Sample Prep & Target Enrichment

Tools & Resources

Feature Articles

Addressing Challenges in Microbiome DNA Analysis

Microbiome sample analysis is commonly confounded by the presence of host-cell DNA in the sample. The NEBNext® Microbiome DNA Enrichment Kit enables enrichment of non-CpG-methylated DNA from samples contaminated with eukaryotic-cell DNA.

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.

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.

Brochures

The NEBNext Sample Preparation Workflow Poster

Posters

Benefits of Illumina^® Library Quantitation with NEBNext^® Library Quant Kit (2015)

High Quality Automation Libraries Prepared from a Broad Range of DNA Input Amounts (2017)

AGBT 2018 Wellcome Trust Sanger Institute poster: Thurston. S., et al. (2018). A Large Genome Centre Core Pipeline Refresh.

Examining Sources of Error in PCR by Single-Molecule Sequencing (2017)

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)

Application of a Novel, Targeted Sequencing-Based Genotyping Approach for Cost Effective Marker Assessment in O. sativa (2019)

EM-seq™ Enables Accurate and Precise Methylome Analysis of Challenging DNA Samples (2019)

Enzymatic Methyl-seq: Next Generation Methylomes (2019)

High-Throughput Screening of 2300 Genetic Markers in S.lycopersicum using the NEBNext Direct Multiplexed Genotyping Approach (2019)

Improving Transcriptome Profiling for Single Cell and Low Input RNA (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)

Uncovering the Cannabis sativa Methylome Through Enzymatic Methyl-seq (2019)

A Customizable Approach for Selective Removal of Abundant RNAs Enhances the Sensitivity of Transcript Detection Across Species

A highly multiplexed target enrichment approach for sample identification and tracking using the NEBNext Direct Genotyping Solution

EM-seq^™ enables accurate and robust methylation detection of cell free DNA and FFPE DNA sample types

Enzymatic Methyl-seq: Next Generation Methylomes

Increasing Power to Detect Low-Frequency Variants Using Dual-Unique Molecular Indices

Increasing Sensitivity of Transcriptome Profiling in Prokaryotic and Eukaryotic Samples by Depleting Abundant RNAs

NEBNext^® Ultra™ II FS DNA: A Robust Enzyme-based DNA Library Preparation Method Compatible with Plant Samples

An improved multiplex targeted amplicon sequencing of SARS-CoV-2 using Oxford Nanopore Technology

Comparison of different sequencing platforms using 480 unique dual indexed libraries for 4 different applications

Enzymatic Methyl-seq enables accurate and robust methylation detection

Improving multiplex targeted amplicon sequencing of SARS-CoV-2 on Illumina platforms

Improving transcriptome analysis by incorporating Unique Molecular Identifiers in RNA-sequencing libraries

Incorporation of Unique Molecular Identifiers (UMIs) into Unique Dual Indexing (UDI) of samples improves the accuracy of quantitative Next Generation Sequencing

Increasing the sensitivity of transcriptome profiling in eukaryote and blood samples by depleting abundant RNAs

Primer-monitor.neb.com – streaming detection and notification of new SARS-CoV-2 variants

Selective removal of abundant RNAs enhances the sensitivity of transcript detection across different prokaryotic and archaeabacterial species

Publications related to NGS Sample Prep & Target Enrichment

Vladimir Potapov, Jennifer L. Ong. (2017) Examining Sources of Error in PCR by Single-Molecule Sequencing. PLOS One; PubMedID: 28683110

Legal Information

This product is covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB).

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 email us 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.

Videos

NEBNEXT^® Ultra II Directional RNA Workflow

Learn more about the streamlined workflow for the NEBNext Ultra II Directional RNA Library Prep Kit.
Size Selection and Cleanup with NEBNEXT^® Ultra II and SPRI beads

This video walks you through the size selection and cleanup steps using the NEBNext Ultra II DNA
Tips for Optimizing DNA Inputs in NGS Library Construction

Optimizing DNA inputs for NGS library prep is an important step, if you want to ensure a high-quality library. Start by following these tips for DNA quantification and assessing purity.
Tips for Optimizing RNA Inputs in NGS Library Construction

Watch as Deyra explains how to optimize your RNA inputs for successful NGS library preparation.
NEBNEXT DIRECT^® Workflow

View our tutorial for help visualizing NEBNext Direct’s unique and enabling workflow.
NEBNEXT DIRECT^® Target Enrichment

Learn about the innovative NEBNext Direct technology for target enrichment for next generation sequencing.
How Library Preparation Affects Sequencing Accuracy

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.
Behind the paper: DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

NEB researchers published a paper in Science highlighting DNA damage as a prevalent source of errors in public cancer databases. Learn about how addressing this damage could improve the detection of low-frequency disease variants.
Challenges and Opportunities for Next Generation Sequencing Target Enrichment

In this webinar, we explore the advantages and limitations of target enrichment, and discuss how NEBNext Direct^®, a novel solution for selective enrichment of genomic targets, addresses these challenges.
NEBNEXT^® Ultra II DNA Library Prep Protocol

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.
12 Quick Tips for NGS Library Preparation

These 12 quick tips for NGS library preparation are a great refresher if you're a seasoned pro, or a great introduction if you're a beginner.