Leiden University Medical Center

Automating Illumina DNA library prep. with flowbot® ONE

Reducing hands-on time with 80%

Many labs performing next generation sequencing choose to automate the liquid handling processes to get a more reliable and efficient library preparation. One of those labs can be found at the Leiden University Medical Center.

With Stefan Boers, Medical Molecular Microbiologist, in the driver’s seat and flowbot ONE as their pipetting partner, their clinical lab has automated the Illumina DNA library preparation kit for whole genome sequencing. This has reduced hands-on time from 125 minutes to 25 minutes, generated good quality genome assemblies as well as consistent and reproducible results.

“Automating our lab was an obvious choice. Especially an NGS workflow has such as extensive library preparation that there is no upside to doing it manually. Choosing flowbot ONE was also an easy decision. It checked all of our boxes,” says Stefan Boers.

The lab is currently using whole genome sequencing for initial identification of rare pathogenic microorganisms, the detection of microbial resistance mechanisms and for epidemiologic tracking of microorganisms within and outside hospital systems.

A user-friendly and flexible setup

The flowbot ONE was easily equipped, programmed, and optimized to perform the Illumina DNA Prep automatically in collaboration with LabHelp – the flowbot ONE distributors in the Netherlands.

For the automation of the Illumina DNA Prep protocol, the flowbot ONE was equipped with a 1-channel 2–200 µl pipetting module, as well as an 8-channel 2–200 µl pipetting module, and the 12-position deck was set up with a heating/cooling device, a magnetic device, and several modules for placement of pipetting tips and tube racks.

“We primarily chose the flowbot ONE because we needed a robot that was flexible and that everyone would be able to use. Our lab technicians are both comfortable using it and switching things around in the protocol. And I have many plans for it in the future and appreciate that it can be easily repurposed for other applications. What we are going to do next is automating our targeted amplicon NGS methods with which we can detect, quantify and identify bacteria and fungi directly from clinical samples,” Stefan Boers explains.


Although we have designed this automated workflow to prepare DNA libraries for small-scale microbial WGS experiments, the easy-to-use software of the flowbot ONE allows automation of most library prep. protocols available for the many NGS and third-generation sequencing applications without the need of advanced programming skills.

Stefan Boers, Medical Molecular Microbiologist

Freeing up 100 minutes to use on more valuable work in the lab is a fantastic outcome. It’s a great way to utilize our lab technicians’ full talents and get more time for tasks such as innovation.

Stefan Boers, Medical Molecular Microbiologist

Efficient library prep. with high-quality data

The lab is sequencing around 8 bacterial strains per week. This is not impossible to do manually, but library prep. is tedious, error prone, and takes a lot of time – time that Stefan Boers wanted to spend on more valuable tasks.

When implementing the flowbot ONE, hands-on time was reduced to 25 minutes compared to the 125 min needed when performing 8 library preps. using the manual workflow.

“Freeing up 100 minutes to use on more valuable work in the lab is a fantastic outcome. It’s a great way to utilize our lab technicians’ full talents and get more time for tasks such as innovation. And, of course, it frees them from spending their energy on tedious work,” says Stefan Boers and adds that the flowbot ONE also enables the lab to easily scale up if needed.

The same experiment revealed that a library prep. workflow on the flowbot ONE generates robust and high-quality DNA libraries.

“Results obtained from 16 library preps. that were performed both manually and automatically showed comparable library DNA yields (median of 1.5-fold difference), similar assembly quality values, and 100% concordance on the final core genome multilocus sequence typing results,” confirms Stefan Boers and adds that the results have been consistent since flowbot ONE was implemented and that no dropouts have been encountered.

Reproducibility of results was confirmed by re-processing eight of the 16 library preps using the automated workflow.


For more data, please see the publication in Scientific Reports 14


Book a demo to see what flowbot ONE can do for your lab.

The installation file of the automated Illumina DNA Prep workflow is also available from Flow Robotics upon request.biobanking with liquid handling robot flowbot ONE