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What to consider when choosing a next-generation sequencing service provider

Published 5 July 2024 by Aoife Holohan

Embarking on a next-generation sequencing (NGS) project requires careful planning and selecting the right service provider can significantly influence your outcomes. Opting for a provider that offers a comprehensive custom workflow ensures seamless management of sample collection, preservation, nucleic acid extraction, quality control, library preparation, sequencing, and bioinformatics analysis through a single point of contact. Utilising free NGS consultations can be instrumental in ensuring your chosen provider aligns with your project's needs, facilitating the design of an optimal experiment and tailored service package. This blog explores essential considerations - from sample preparation to bioinformatics analysis - to assist you in making informed decisions and achieving high-quality results for your research.

NGS consultation and knowledge

When planning an NGS project, it is crucial to find a service provider that offers the specific type of NGS you need and can work with your samples. A brief search will reveal numerous providers, such as those specialising in RNA sequencing or metagenomics sequencing. Assess the capabilities of your chosen provider, considering factors like sample volume, equipment access, and deadline adherence. Look for a supplier whose projects start with a consultation to design an optimal workflow and agree on a tailored NGS service package. 

Customer service and collaboration

When selecting an NGS service provider, consider the quality of customer service you will receive. This is especially crucial if you are working with difficult sample types or lack NGS experience. Confidence after your initial consultation is key, as is ongoing support throughout the sequencing process. By the end of the consultation, you should feel assured that both of these aspects will be covered by the provider. 

Sample preparation and collection

Quality samples are crucial for quality NGS results, making sample preparation a key factor. Proper initial handling significantly impacts the nucleic acid quality, which in turn affects the data produced. However, control over sample collection and handling isn't always feasible, especially with archived samples where concentration and quality may be concerns. When choosing an NGS service provider, consider their sample preparation standards. For archived samples, ensure the provider uses high-quality extraction kits. If sample collection is pending, opt for a provider who offers pre-collection handling recommendations and necessary technology for collection and preservation, such as those that inactivate pathogens or protect nucleic acid content. 

Sample submission and shipping

Shipping biological samples on dry ice can be stressful, especially over long distances. Choose a service provider that offers helpful sample submission and shipping advice. For international shipments, select a provider who monitors the shipment and provides detailed shipping instructions to ensure your samples arrive in good condition. Pay attention to specifics like the best day to ship and the amount of dry ice needed. Ensure the shipping arrangements are economical and time-efficient. Selecting a provider who prioritises these details will save you future stress. Additionally, look for a supplier that can offer support with customs and export documents.

Nucleic acid extraction

For researchers lacking time or resources for nucleic acid extractions in their lab, selecting a service provider offering this service within their NGS workflow can be advantageous. Particularly with complex sample types like ultra-low input liquid biopsies or FFPE samples, an experienced provider can save significant time, money, and effort. Look for a service provider with experience of nucleic acid extraction from diverse sources including tissues, cells, and biofluids, with specialised capabilities in challenging samples like FFPE slides and microdissections if that is something you require. If your sequencing needs are for microbiomics, a provider that can offer unbiased lysis of bacteria, archaea, fungi, and viruses is important to find.

Quality control and library preparation

Ensuring rigorous quality control throughout every phase of your project is critical. When choosing an NGS service provider, it's essential to understand their quality assurance protocols for your samples. Whether you conduct the nucleic acid extraction yourself or send your samples to the provider for extraction, selecting a provider who evaluates QC data for library preparation suitability is crucial. For samples with low concentration or challenging characteristics, a provider who shares QC results before sequencing can be advantageous. Many providers will specialise in preparing libraries from even the most challenging or low-quality samples, employing library preparation solutions tailored to specific experimental goals, integrating quality control measures at every stage. Choosing a provider that has access to their own proprietary library preparation kits can expedite this step, as well as allowing for customisation of the protocol for challenging samples.


The quality and reliability of sequencing results hinge greatly on provider expertise in selecting the appropriate sequencing platform and protocols for your specific research goals. A proficient provider not only ensures accurate data generation but also optimises sequencing depth and coverage, thereby enhancing the overall quality of results. In modern genomic research, each sequencing project demands a nuanced approach to yield meaningful and actionable insights. 

Bioinformatic Analysis

Choosing an NGS service provider often hinges on whether they include advanced bioinformatics analysis in their offerings, which is crucial depending on your research requirements and familiarity with raw data. It's essential to clarify beforehand what specific figures and graphs are part of their bioinformatics service report, as these details can vary significantly between providers. To avoid assumptions about the inclusion of certain analyses like volcano plots, request a sample service report from the provider to ensure it meets your needs. For research projects intended for publication, it's vital to select a provider capable of delivering both raw sequencing data and publication-ready figures. Additionally, opting for a provider with bioinformatics technical support ensures you can seek assistance and guidance. Look for a provider whose offerings encompass in-house sequencing data analysis, including standard options, customisable analyses tailored to specific needs, and the development of bespoke pipelines.

Data security

How a provider will process, store and transfer your data is important for security, particularly if your samples originated from patients, as maintaining patient confidentiality is crucial. From a research perspective, ensuring the integrity and confidentiality of NGS data is vital for the reliability of scientific research and building public trust in the advancements of genetic technologies. Options for data transfer can include cloud transfer or physical hard drives. Ask your chosen provider about their storage methods and what policies they have in place for data purging after certain periods of time. 

Cost of quality

When selecting an NGS service provider, it's crucial to balance cost with quality. While price is a significant factor in decision-making, it directly reflects the level of service you'll receive. Choosing solely based on low cost may compromise essential factors. Keep these considerations in mind to ensure you find a provider that meets your needs and delivers high-quality, impactful results. 

If you are looking to start your own NGS project soon, you can explore the service providers we work with.