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Next Generation Sequencing and Genotyping by Sequencing

Next generation sequencing (NGS) and genotyping by sequencing (GBS) support scalable genomic analysis across research, breeding and molecular biology applications. From targeted GBS with Amp-Seq One and medium-density sequencing with Flex-Seq™ to high-density Capture-Seq workflows and 16S metagenomics, we help scientists develop reliable sequencing workflows with custom oligos, sequencing adapters and index primers.

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Young crop seedlings growing in a field, representing plant breeding, agrigenomics research and sequencing-based crop improvement applications.

Building scalable NGS and genotyping workflows

NGS supports the generation of high-density genomic data across agrigenomics, breeding and molecular biology applications.

From targeted sequencing and genomic selection to metagenomics and 16S rRNA sequencing, NGS provides the scale and flexibility needed to generate actionable genomic insights.

Reliable sequencing workflows depend on effective library preparation, multiplexing and target enrichment strategies. We provide the expertise and oligonucleotide components required to support NGS and GBS workflows from library construction through to demultiplexing and downstream analysis.

Browse custom oligos, adapters and index primers

Scientists and organisations using next generation sequencing

  • Genomics researchers

  • Molecular biology laboratories

  • Plant breeding programmes

  • Livestock breeding organisations

  • Agricultural biotechnology companies

  • Population genetics researchers

  • Genomic selection teams

  • Marker-assisted breeding programmes

  • Microbiome laboratories

  • Metagenomics researchers

  • Sequencing core facilities

  • Targeted sequencing service users

Solving library preparation, targeting and genotyping challenges in next generation sequencing

NGS and GBS performance is influenced by factors including DNA quality, library preparation, target enrichment, multiplexing and sequencing depth. Addressing these challenges can improve on-target performance, marker recovery and SNP calling confidence.

Optimising library preparation workflows

Library preparation is a critical step in any sequencing workflow. Factors such as DNA quality, fragmentation, adapter ligation, target specificity and library complexity can influence sequencing performance, coverage uniformity and downstream data quality. Understanding these variables helps reduce workflow bottlenecks and improve sequencing success.

Managing multiplexing and sample indexing

Large sequencing projects often require thousands of samples to be processed simultaneously. Effective use of sequencing adapters, dual-index primers and barcoding strategies supports accurate sample identification and efficient demultiplexing across highly multiplexed sequencing runs.

Selecting the right targeted sequencing approach

Amplicon sequencing, probe-based targeted sequencing and hybrid capture each offer different advantages in terms of marker density, flexibility and scalability. Choosing the most appropriate approach depends on project objectives, target density, required read depth and the level of genomic resolution needed for downstream analysis.

Balancing read depth and target coverage

Achieving sufficient read depth, specific target and sample coverage is essential for reliable SNP calling, marker recovery and accurate genotyping across large sample cohorts. Insufficient sequencing depth can limit confidence in downstream analysis, particularly in large-scale genotyping projects.

Scaling genotyping programmes efficiently

As breeding programmes expand, sequencing strategies must deliver the required marker density and data quality while maintaining throughput and cost efficiency across large populations.

Designing robust 16S rRNA sequencing studies

Microbiome and metagenomics projects require careful consideration of marker-gene selection, including 16S rRNA targets, sequencing strategy and downstream bioinformatic analysis requirements. Appropriate experimental design helps maximise the value of 16S rRNA sequencing data and supports meaningful biological interpretation.

When should I use next generation sequencing or genotyping by sequencing?

The optimal sequencing strategy depends on your application, marker density requirements and throughput objectives. Understanding the strengths of different sequencing strategies helps deliver the right balance of performance and flexibility.

Discuss your sequencing project
DNA gel electrophoresis analysis in a molecular biology laboratory, supporting DNA quality assessment and sequencing workflow preparation.

Choose Amp-Seq One for targeted GBS workflows

Amp-Seq One provides a one-stage targeted genotyping-by-sequencing workflow designed for industrial-scale genotyping applications. It is well suited to projects requiring defined marker panels, high sample throughput, cost-effective genomic selection and marker assisted selection.

Use Flex-Seq™ for medium-density targeted sequencing

Flex-Seq™ combines high marker recovery, high on-target sequencing rates and compatibility with existing genotyping datasets, enabling breeders to expand or refine marker panels while maintaining continuity with historical data.

Select Capture-Seq for high-density target enrichment

Capture-Seq uses probe hybridisation-based target enrichment to characterise hundreds of thousands of genomic targets across complex genomes, supporting high-density marker discovery, haplotyping and genomic analysis.

Applications and technologies supporting
NGS and GBS workflows

Related Products and Solutions

Targeted Genotyping by Sequencing

Amp-Seq One

A one-stage targeted genotyping-by-sequencing workflow developed for industrial-scale breeding and agricultural biotechnology programmes. Supports genomic selection, marker-assisted breeding and parentage testing applications.

Amp-Seq One

Targeted Sequencing

Flex-Seq™

High-throughput probe-based targeted sequencing platform that can target tens of thousands of markers while maintaining compatibility with legacy datasets and evolving breeding programmes.

Flex-Seq™

Hybrid Capture

Capture-Seq

Hybridisation-based target enrichment platform for characterising hundreds of thousands of genomic targets and generating data for genomic selection, marker discovery and haplotyping applications.

Capture-Seq

Metagenomics

16S rRNA Sequencing Services

Amplicon-based metagenomics services supporting microbial community profiling, taxonomic classification, bacterial community characterisation and microbiome research studies.

16S rRNA Sequencing Services

Featured Resources

Basket of freshly harvested potatoes in a field, representing potato breeding and crop improvement programmes aimed at developing disease-resistant varieties.

How Potato Breeders Use Flex-Seq™ in the Battle Against Late Blight Disease

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Soybean plant with developing pods being inspected in the field, illustrating genotyping-enabled crop breeding and trait selection programmes.

In-House Targeted GBS Installation with Amp-Seq One

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Plant tissue sample in a laboratory microcentrifuge tube, representing agricultural next-generation sequencing and genomic analysis workflows.

Agricultural NGS Technologies and Services

Solution Overview
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Why choose LGC Diagnostics & Genomics

We partner with scientists to overcome sequencing workflow and genotyping challenges, helping them implement reliable library preparation, enrichment and genomic analysis strategies.

Expertise across NGS and GBS workflows

Access expertise spanning targeted sequencing, hybrid capture, amplicon-based genotyping, metagenomics and high-throughput agrigenomics workflows.

Support for complex sequencing programmes

We support projects requiring library preparation, target enrichment, sequencing workflow development and large-scale genomic analysis.

One partner across diagnostics and genomics

Access custom oligos, sequencing expertise and targeted sequencing capabilities through a single trusted partner.

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Genomics goes mainstream across research and healthcare

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Global reach

144

Countries served through our global diagnostics and genomics network.

Customer community

37,000+

Customers supported across diagnostics, genomics and life science applications.

Frequently asked questions

What is next generation sequencing and how does it work?

Next generation sequencing uses massively parallel sequencing technologies to sequence many DNA fragments simultaneously. Samples are prepared as sequencing libraries before generating sequence data for downstream analysis.

What goes into NGS library preparation?

Library preparation involves converting DNA or RNA samples into sequencing-compatible libraries. Depending on the workflow, this may include DNA fragmentation, end repair, adapter ligation, incorporation of sequencing adapters and index primers, and target enrichment through either amplicon-based amplification or hybridisation-based capture. These steps generate sequencing-ready libraries for multiplexed sequencing and downstream analysis.

What are sequencing adapters and index primers?

Sequencing adapters enable DNA fragments or amplicons to be incorporated into sequencing libraries, while index primers provide sample-specific barcodes that support multiplexing, demultiplexing and tracking of individual samples within a sequencing run.

What is genotyping by sequencing?

Genotyping by sequencing uses NGS workflows to identify and genotype genetic variation across large sample populations, supporting applications including genomic selection, marker discovery, parentage testing and marker-assisted breeding.

When should you use GBS instead of an array or PCR genotyping?

GBS may be preferred when projects require greater marker flexibility, SNP discovery capabilities or scalable marker densities not available through fixed-content genotyping arrays.

What is the difference between amplicon sequencing and hybrid capture?

Amplicon sequencing relies on amplification of genomic targets before sequencing, whereas hybrid capture uses probe hybridisation and target enrichment to recover regions of interest from sequencing libraries.

What drives the cost per sample in an NGS run?

Sample throughput, marker density, sequencing depth, target enrichment requirements and sequencing strategy can all influence the cost per sample of an NGS workflow.

Need help planning your next sequencing project?

Whether you are evaluating targeted sequencing technologies, implementing a genotyping-by-sequencing workflow, developing a marker panel or optimising library preparation, our scientific experts can help identify the most effective approach for your application.

Talk to our expertsBrowse custom oligos, adapters and index primers