Internship Bioinformatician Nanopore Sequencing Technology

Since 2019, Naktuinbouw has been at the forefront of using third-generation Nanopore sequencing (ONT) technology to detect viral and bacterial pathogens in plants. Our diagnostics department relies on this cutting-edge technology to help growers diagnose plant diseases and to design TaqMan assays for the ornamental crop sector. Our in-house sequencing facility is powered by advanced bioinformatics tools and pipelines, delivering complete, actionable results. 

ONT technology continues to evolve rapidly, with ongoing improvements in flow cells, library preparation kits, and basecalling algorithms. Since the pandemic, the field of virus identification using long-read sequencing has also seen major advances in bioinformatics algorithms, tools, and pipelines. 

With these exciting developments, we’re ready to rethink and upgrade our in-house bioinformatics pipeline. Our goal is to integrate state-of-the-art tools, deliver robust statistical insights into sequencing quality and classification, and dramatically shorten the time from sample to diagnostic result—crucial for our department’s efficiency. 

What you’ll do: 

• Dive into the latest literature on viral classification pipelines for ONT 

• Work closely with our researchers to identify and implement improvements in our current pipeline 

• Brainstorm and strategize with the team to boost both research quality and operational efficiency 

• Test and integrate new tools into our evolving de novo pipeline 

• Support our programmers in enhancing the adapter identification system (built in Rust)—no Rust experience needed, just your curiosity! 

• Benchmark Epi2me and other nanopore pipelines using validated datasets 

• Explore and help set up pan-genome visualization tools on our server 

• Collaborate on automating tools and pipelines, moving from research to real-world application 

• Assist in deploying pipelines and databases on our local GPU server and partially in the Azure cloud 

What we’re looking for: 

• You’re currently pursuing a bachelor’s or master’s degree in Bioinformatics 

• You have an eye for detail and solid coding skills for data analysis 

• You’re passionate about research quality, reporting results and making good overviews 

• You’re eager to test and benchmark new algorithms and tools 

• You’re patient, organized, and enjoy working in a collaborative team 

Depending on your level (bachelor’s or master’s) and your availability (6 or 9 months), we’ll tailor the project goals to fit you. 

You’ll work side-by-side with our computational team at Naktuinbouw—an amazing chance to dive into the heart of Nanopore technology, plant pathogen surveillance, and research. 

Project Lead & contact person: Sanchari Sircar, S.Sircar@naktuinbouw.nl 

Department: R&D, Bioinformatics 
Date: Jan 2026