Optimising NGS Experiment Design with Expert Consultancy

Many NGS projects underperform not because of sequencing quality, but due to early design choices, such as library preparation methods, sequencing depth, or unsuitable controls. These issues are often difficult or impossible to resolve later.

At NextGenSeek, we offer pre-experiment consulting and bioinformatics expertise to help you plan NGS experiments that produce reliable, interpretable data from the beginning.

Our aim is to help you avoid common pitfalls and make informed decisions before starting sequencing.

Key considerations for designing NGS experiments

Our consultancy focuses on the critical choices that shape data quality and downstream analysis.

Coverage depth

Sequencing depth should be guided by your biological question, sample type, and analysis goals — not by generic recommendations. We assist in determining an appropriate coverage strategy that balances sensitivity, statistical power, and cost.

Read length selection

Read length significantly impacts mapping accuracy, variant detection, transcript assembly, and splicing analysis. We advise on optimal read lengths based on:

  • Target region complexity

  • Genome or transcriptome size

  • Planned downstream analysis (e.g. variant calling, RNA-seq, metagenomics)

Paired-end reads vs. single-end sequencing

Paired-end sequencing provides additional information for many applications, but it is not always necessary. We help you decide when paired-end data is essential and when single-end sequencing is sufficient, ensuring resources are used efficiently.

(See our two educational videos on paired-end versus single-end sequencing.)

Selecting the right sequencing platform

With multiple sequencing technologies available, choosing the most suitable platform can be challenging. We advise based on:

  • The type of data you aim to generate

  • Required resolution and throughput

  • Budget constraints

Because NextGenSeek does not provide sequencing services, our recommendations are entirely technology-agnostic. This allows us to provide objective advice, ensuring the chosen platform supports your scientific goals rather than introducing unnecessary cost or complexity.

Library preparation strategy

Library preparation choices strongly influence data quality and bias. We help select appropriate kits and workflows by considering:

  • Sample type and quality

  • Sequencing platform compatibility

  • Study-specific requirements

Careful planning at this stage reduces artefacts, dropouts, and technical bias.

Controls and experimental structure

Robust controls are essential for reproducible results. We assist in defining appropriate:

  • Biological replicates

  • Technical controls

  • Positive and negative controls

tailored to your experimental design and analysis plan.

Cost-efficiency without compromising quality

Budget constraints are a reality for many projects. We help you evaluate trade-offs between cost and data quality, ensuring sequencing resources are used where they matter most — without compromising scientific validity.

Why pre-experiment consultation matters

Many issues that appear during analysis originate from early design choices. Inadequate planning can result in data that is difficult to interpret, statistically underpowered, or unsuitable for the intended biological question.

Pre-experiment consultation helps ensure that your study is designed with downstream analysis in mind, reducing risk and increasing the likelihood of meaningful results.

Get in touch

NextGenSeek provides tailored NGS consultancy for projects across a wide range of research areas, including cancer genomics, microbiome research, and drug development.

If you are planning an NGS experiment or reassessing an existing design, we’re happy to discuss your project and help you develop a robust experimental strategy.

Contact us for NGS consultancy or for general science consultancy.