Whether a lab is just starting up using next-generation sequencing (NGS), or needs to scale its capacity, one looming question is: “Do I want to do my sequencing in-house, or do I want to use sequencing services?”

There are good reasons that support either path and numerous factors to consider. Ultimately, the choice between outsourcing NGS or performing it in-house hinges on the specific needs of the research team and your lab operation. There is no one-size-fits-all solution.

In this blog, we highlight what should be considered when deciding what makes the most sense for your project goals.

Considerations for In-House NGS

Utilizing in-house sequencing resources comes with many benefits, such as:

  • The ability for labs to process and validate unusual specimen types that might not be accepted by service laboratories
  • Intellectual property considerations and proprietary data protection
  • Lower cost per sample, especially if equipment and capacity are already in place
  • Potential for quicker turnaround times compared to outsourcing, although some service providers can provide next-day results for certain sample types

When a project aligns with sequencing platforms and pipelines already established, the researcher can likely achieve their goals quicker and more cost efficiently by staying inside their facility.

However, in-house NGS can bring its own set of challenges.1 For example, setting up NGS infrastructure can be difficult and expensive. If the workflow to handle the projects is not already in place, a lab faces the expenses of purchasing new equipment, hiring more employees, scaling up training, and bioinformatic pipeline development, etc.

When to Opt for Outsourcing NGS Services

Outsourcing NGS can be a valuable option for labs for a variety of reasons:

  • Ability to complete large projects exceeding the lab’s normal capacity
  • Reduces the need for large capital equipment expenditures or new headcount
  • Takes advantage of expert skills, capabilities, or analysis pipelines not currently available in-house
  • Cost per sample can potentially be less expensive than in-house sequencing if the service provider has an extremely efficient workflow and high capacity sequencers2
  • Turnaround time can actually be faster in instances where the lab would otherwise wait to fill up a flow cell prior to running the sequencer to keep costs reasonable

In many ways, the advantages and disadvantages regarding outsourcing your sequencing are opposite to keeping your samples in-house. Allowing your samples and data out of your direct control opens your lab up to potential data security issues, which is the biggest concern on many companies’ minds.

An additional consideration is whether the provider handles the sample type you provide and the analysis you need. What portion of your overall workflow are they replacing, and can they do it cheaper, faster, or better than your lab can?

Data Considerations

Regardless of your choice for in-house or outsourced sequencing, data analysis and storage will be a concern.3,4 Depending on the service provider, many of your analysis needs can potentially be handled by the outside contractor, albeit potentially at a higher price per sample. These service labs are also unlikely to store your data long-term, so even in a “complete” solution, the end-user still needs to plan for how to keep their data for future reference.

Cloud services, such as Illumina BaseSpace, Microsoft Azure, or Amazon Web Services (AWS), are popular solutions for handling both the compute power required for analysis and the storage of the data after the fact. A lab should think critically about their budget as the amount of data accumulated from multiple projects can become a significant long-term storage cost.

Much like the decision to outsource the actual sequencing or perform it in-house, the options for data analysis and storage don’t necessarily have a right or wrong answer. It comes down to a careful analysis of your individual cost structure, capacity, and concerns about data security.

A Case Study – Plasmid Sequencing

Consider a situation with a relatively simple sample type – plasmid construction for synthetic biology applications. Here, labs can see a range of throughput from just a few per week to thousands that need to be sequenced at one time. Analysis is generally restricted to relatively straightforward alignment or de novo assembly, and some analysis pipelines are publicly available (although the quality of the assemblies may vary, or the user may wish to customize to their specific needs).

In most cases, turnaround time for outsourcing plasmid sequencing is fast, with results typically returning within 1-2 business days after receipt of samples. Costs can be very reasonable and likely cheaper than what can be achieved in-house unless the user already has a very efficient workflow established. One platform used to achieve lower cost and faster turnaround of plasmid sequencing is Oxford Nanopore. While the lower throughput is sufficient for many users, others may be wary of the higher error rates and lower overall data quality compared to that of the Illumina platforms.

In deciding whether to perform plasmid sequencing in-house or via outsourcing, the primary decisions tend to be related to needed throughput, cost per sample, turnaround time, data quality, and data security. In the end, most labs will choose one solution and stick with it out of necessity. Switching back and forth would likely result in using different prep methods or sequencers, generating variability in data quality.

But, what if you had the option of using the same methods regardless of doing the work in-house or using a provider, enabling the highest flexibility possible?

How seqWell Can Help

At seqWell, we provide the best of both worlds for plasmid sequencing customers.5 Thanks to our ExpressPlex Library Prep Kit, preparing anywhere from a few samples to thousands at one time can be achieved in just a few hours.6 Prepping a single plate of 96 or 384 samples for sequencing takes 90 minutes, with just 30 minutes of hands-on time.

In addition, there are no primers or barcodes to buy and maintain – everything is included in one simple kit with the easiest workflow available anywhere.

Parallel path processing of multiple plates is easy and, with utilization of readily-available liquid handling platforms, turnaround of extracted DNA from plasmid samples, including library prep, sequencing, and assembly analysis can happen in as little as 24 hours from start to finish. And, all of this can be accomplished on Illumina sequencing platforms, ensuring the highest quality data possible.

Due to the flexibility and ease-of-use of the ExpressPlex Library Prep Kit, labs don’t necessarily have to choose between analyzing samples in-house or outsourcing. seqWell has designed a system that provides the library prep kits directly to you for day-to-day use in your lab. But, if throughput needs outgrow internal capacity or individual projects cause short-term spikes in throughput that don’t justify investments in capital equipment, users can turn to seqWell to provide services that use exactly the same prep methods and return data of the quality matching your current standards.

With the seqWell ExpressPlex plasmid sequencing services, we handle all aspects of whole-plate library preparation, sequencing, and data processing on-site, including de novo plasmid assembly via our SNAP pipeline. Our process for submitting samples is straightforward, and all data is securely delivered to you via a web server for effortless access.

Our team has been performing fully-assembled plasmid sequencing services for clients for almost a decade so you can rely on our extensive NGS experience and expertise. We continue to innovate and make plasmid sequencing faster and easier every day, and have made these innovations available to you to use in your own lab as well. So, whether you want to want to perform your plasmid sequencing in-house, outsource to a fast and reliable provider, or have the flexibility to do either as your needs dictate, seqWell should be your go-to source to make it all happen.

Contact us today and let seqWell’s sequencing experts get the work done as efficiently as possible. Spend your valuable time on discovery and analysis, not sitting at the bench. You have more important things to do!


  1. Computational and Structural Biotechnology Journal | Challenges in the Setup of Large-scale NGS Analysis Workflows
  2. BiteSizeBio | Kiss your samples goodbye: Outsourcing your Next-Gen experiment
  3. ThermoFisher Scientific | NGS Data Analysis for Illumina Platform—Overview and Workflow
  4. Practical Laboratory Medicine | Practical estimation of cloud storage costs for clinical genomic data
  5. seqWell | Plasmid Sequencing Services
  6. seqWell | ExpressPlex Library Prep Kit