At BaseClear, we have been working with Oxford Nanopore Technologies for nearly a decade. As one of the first certified Oxford Nanopore service providers in Europe, we have used nanopore sequencing to tackle a wide range of biological challenges, from complex environmental metagenomes to large eukaryotic genomes.

Recently, a client in the environmental sector challenged us with something big: sequencing hundreds of soil samples with the goal of assembling genomes of previously undescribed microbial species. The scientific scope was significant, and it came with equally demanding logistical requirements.

This blog post explores how we expanded our Oxford Nanopore sequencing capacity in close partnership with the technical and commercial teams at Oxford Nanopore Technologies, scaled up our infrastructure and workflows, and built a future-ready service capable of supporting advanced metagenomic discovery at scale.

Meeting the challenge: soil metagenomics at scale

Soil metagenomics is a data-intensive and biologically complex area of microbiome research. With its high microbial diversity and abundance of unknown organisms, it demands sequencing technologies that can capture full genomes without relying on references. Short reads can offer a snapshot. But for truly novel discovery, reads of unrestricted length, like those provided by Oxford Nanopore sequencing, are essential.

Our client needed raw sequencing data that would enable de novo assembly of microbial genomes, many of which had never been sequenced before. They would handle the downstream analysis, but they needed sequencing data they could trust.

We already had Oxford Nanopore devices in-house, but not at the scale required for this project. This kicked off a rapid collaboration with Oxford Nanopore Technologies to grow our capacity and tailor our systems for high-throughput, long-read metagenomics.

Scaling with Oxford Nanopore: infrastructure and partnership

Scaling up our nanopore sequencing setup required more than just installing additional devices. It meant redesigning parts of our workflow to handle larger sample volumes, more frequent sequencing runs, and tighter turnaround times than before, without sacrificing quality.

This is where close collaboration with Oxford Nanopore Technologies became essential. Rather than simply delivering hardware, their team worked closely with us to develop a configuration and workflow that fit the structure of our service lab. We scaled up PromethION usage, optimised library prep steps, and refined data delivery to match client expectations.

At the same time, we began integrating nanopore sequencing into our laboratory information management system (LIMS). This ongoing effort is designed to enable full traceability, automate tracking, and prepare for future GMP-like offerings.

For Céline Miganeh Hadi (Associate Director, Field Applications Scientists at Oxford Nanopore Technologies), a member of the team supporting BaseClear: ‘At Oxford Nanopore, we have a dedicated team of experts to support our users, such as BaseClear, throughout the sequencing workflow, including workflow optimisation and automation, data management/storage and analysis, scaling to needs, and high-throughput project management. We are proud to play a part in helping our customers achieve their goals’.

Results: quality data, lasting trust

Our role in the project was focused on sequencing and quality control. While the client carried out their own bioinformatics, the data quality enabled them to assemble strain-level genomes directly from complex soil samples, something that is difficult to achieve with short-read sequencing alone.

Importantly, the client has since returned for additional services, including upstream sample processing and expanded sequencing requests. This kind of return engagement reinforces that scaling isn’t just about meeting one-time demand; it’s about building trust through consistency and quality.

Why our partnership matters

For a service provider like BaseClear, Oxford Nanopore Technologies stands out not only for its technology but for its collaborative mindset. Oxford Nanopore has been uniquely open to adapting its support and tools to fit our workflows. Whether it’s troubleshooting sample prep or supporting our LIMS integration, the team at Oxford Nanopore Technologies has been consistently accessible, fast, and transparent — key traits in any innovation partner.

According to Roel Sprengers (Associate Director, Regional Sales at Oxford Nanopore Technologies), who has been supporting the collaboration with BaseClear: ‘BaseClear is a highly experienced user of Oxford Nanopore technology, offering nanopore sequencing as a service. Providing this sort of service is key for technology accessibility and, therefore, our overall vision: to enable the analysis of anything, by anyone, anywhere. I am really looking forward to our continued collaboration and many more projects’.

Looking ahead: future-ready services

Thanks to this successful scale-up, BaseClear now operates a production-ready Oxford Nanopore sequencing service built for high-throughput, traceable delivery. As we finalise LIMS integration, Oxford Nanopore technology remains central to our plans for the future.

By the end of 2024, our service ramped up to process over 1,000 flow cells in just three months, powered by three PromethION 24 devices. This milestone underscores our ability to support large-scale, time-sensitive projects.

With this infrastructure now in place, we are ready to support a growing range of complex projects, whether they involve regulatory-compliant microbial genomics, large-scale genome assemblies, or high-resolution metagenomics in agricultural and environmental contexts.

Ultimately, the Oxford Nanopore platform proved not only capable but flexible, able to adapt to new challenges and scale in step with project needs.

Feel inspired to establish or expand your Oxford Nanopore platform offerings? Check out our platform page to find out more.