Automated next generation sequencing (NGS) library preparation

Next-generation sequencing (NGS) has revolutionized genomic research by empowering researchers to sequence genomes at speed.

Why Automate NGS Library Prep?

Automated instrumentation is already driving genomics forward, as labs face ever-growing sample volumes and research demands. Yet, many workflows still rely on manual pipetting, mixing, dispensing, incubating, and shaking—repetitive tasks that can sap both time and researcher expertise. By automating these steps, you can:

Boost throughput with 96- and 384-well plate formats
Improve accuracy & reproducibility through precise liquid-handling
Reduce per-sample costs via miniaturization and lower reagent use
Free experts to focus on experimental design and data analysis

Because reagents like polymerases and fluorescent dNTPs can account for a large share of your per-sample spend, miniaturization powered by robotics is key to breaking through the “$100 genome” barrier.

Consideration	Impact
Footprint & Bench Space	Compact, multi-functional platforms eliminate duplicative equipment—saving real estate and lowering environmental impact.
Software Usability	Intuitive GUIs remove the “robot-fear” factor, enabling any researcher to run protocols without vendor intervention.
Protocol Flexibility	Cloud-shared libraries and user-editable methods accelerate deployment of new chemistry and custom assays.
Capital vs. Consumables	A modest upfront investment pays for itself in reduced tip, plate, and reagent waste—and in saved researcher hours.
Scalability & Throughput	Modular designs let you start small and scale to hundreds—or thousands—of libraries per week.

Input QC & Quantification

Automated spectrophotometers and fluorometers integrate with liquid handlers to verify input DNA/RNA concentration and integrity before fragmentation.

Fragmentation & End-Repair

Enzymatic or acoustic shearing modules on-deck ensure consistent fragment sizes, followed by end-repair and A-tailing in a temperature-controlled incubator.

Adapter Ligation & Cleanup

Robotic pipetting adds indexed adapters, then magnetic‐bead purification stations remove excess adapters and small fragments—critical for cluster generation on sequencers.

Final QC & Normalization

Integrated capillary electrophoresis or microfluidic analyzers assess final library size distribution, while software-driven normalization ensures equimolar pooling.

Automated biostorage boosts productivity

Automated cherry picking saves facilities hours of highly qualified researcher and technician time in comparison to manual searching, dramatically increasing productivity. With a single arktic typically replacing two to three manual freezers, facilities can improve cost-efficiency and benefit from significant workflow improvements.

The Democratization of Automation

A new generation of affordable liquid-handling platforms is transforming access to automation across research environments. With intuitive drag-and-drop software, cloud-based protocol repositories, and modular, plug-and-play accessories, these systems are no longer limited to high-budget institutions. They are empowering individual researchers and small labs to implement automation without needing in-house robotics expertise. By removing both technical and financial barriers, this new wave of technology enables scientists to scale experiments, share and adapt protocols within collaborative networks, and maintain full control over workflow customization—all while ensuring sample traceability and consistency.

Overcoming the Sample Prep Bottleneck

NGS runs are getting faster and cheaper—sequencer throughput doubles every 12–18 months—yet library prep remains the rate-limiting step. Automation solves this by:

Miniaturizing reaction volumes (down to sub-microliter scale) to slash reagent use by 50–80%
Parallelizing steps across hundreds of samples to deliver data faster
Standardizing workflows to meet reproducibility demands for clinical and translational research

Case study

Evaluation of a novel, compact, automated
liquid handler for NGS library preparation

In recent years, advancements in the field of next-generation sequencing (NGS) have improved our access to detailed genomic information. Samples that are destined for sequencing need to be processed into libraries before they can be loaded onto a machine that performs the sequencing run.

In this poster, we evaluate the use of firefly, a novel and highly compact liquid handler, for the automation of NGS library preparation workflows. firefly is an extremely compact automated liquid handling platform, measuring 66cm x 56cm x 78cm (width x depth x height), making it easy to place in almost any laboratory that wants to improve efficiency by automating manual workflows.

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Related products

Our range of liquid handling products provide ease of use, reliable solutions for automated NGS Sample Preparation.

firefly^®

Innovative all-in-one liquid handling brings together multiple technologies within a single compact design for more efficient library and sample preparation workflows and maximum output. Underpinned by powerful, intuitive software, firefly unlocks the potential of automation for all to accelerate genomic research.

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dragonfly^® discovery

dragonfly discovery enables innovative, low volume reagent dispensing across a broad range of applications including genomics, assay development, and 3D cell cultures. Highly repeatable and accurate low volume dispensing, rapid large volume dispensing, and ultra-low dead volumes allow researchers to minimize reagent costs, save time, and standardize assays for superior quality data.

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mosquito^® genomics

Next Generation Sequencing (NGS) costs have reduced, NGS sample numbers have dramatically increased leading to a sample and library preparation bottleneck. Harnessing automation and miniaturization enables researchers to realize the full benefits of the genomics revolution. Our solutions dramatically improve productivity and reduce cost per sample for applications such as PCR, quantification and normalization, synthetic biology and a range of NGS library preparation methods supporting single-cell genomics, transcriptomics, microbiome and metagenomics, agbio, clinical genomics and pathogen surveillance.

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apricot

apricot instrumentation provides accurate, precise and intuitive automated liquid handling technology for convenient general use across your entire team. The small footprint designs allow laboratories to maximize available space without compromising on pipetting performance.

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