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Scalable flexible solutions that reduce manual touchpoints and maximise resources

Automating NGS library preparation

Why you need a solution

Library preparation is involved in any number of next generation sequencing (NGS) processes, from RNA sequencing to cancer panels. It often takes highly trained scientists a considerable amount of time, creating bottlenecks and a frustrated, underutilised workforce.

Automating library preparation – either as part of an end-to-end NGS workflow or as an independent workcell – is easy with the right solution.

For labs with limited space, or resources, or those looking to increase throughput without adding additional staff or instrumentation, open, integrated automation (OIA) solutions can unlock untapped potential.

LINQ is our first OIA platform and with it, you can create fully automated library preparation workflows with amazing results.

The benefits of automating library preparation

More walkaway time

Fewer deck setups, 99% reduction in manual touchpoints and end-to-end connectivity means LINQ does the work while your lab team innovate.

Simplified workflows

End-to-end automation with LINQ can include extraction, library preparation and quality control with or without separation – LINQ is designed for you.


Optimised resources

LINQ can integrate existing equipment and optimise its use, helping you get the most from your current investments and any you make in the future.

Benchtop automation vs. LINQ solution

A lab running a daily RNA sequencing protocol using two large liquid handlers, requiring manual attention for plate handling and deck set ups would see manual touchpoints almost eliminated, deck setups reduced significantly, and throughput doubled – with no additional liquid handlers needed.

Optimising pre and post-PCR in RNA sequencing

For those running an RNA sequencing protocol daily, within normal working hours, across two pre and post-PCR laboratory spaces with manual plate handling and deck setups, a lab could expect to save time and scale up with no additional instrumentation or staff needed with a LINQ set up like this:

3D renders showing a pre-PCR workcell set up on the LINQ bench
3D renders showing a post-PCR workcell set up on the LINQ bench

Pre and post-PCR library preparation workcells integrated and automated on the LINQ Bench

The potential impact of this solution vs scaling x2 throughput with benchtop automation

Manual hours
per week

Desk set-ups
per week

Additional liquid
handlers required

More about LINQ

Automata LINQ supports labs at every level of automation by combining three components into one powerful solution:

An automated lab bench that fits into the same space as a regular lab bench, yet allows the full automation of workflows.

The robotic automation system enables the automated transfer of labware between benchtop instruments.

The Automata LINQ bench can integrate with a variety of instruments and the modular design allows it to be adapted for any workflow or any existing environment.


Easily configured to your lab space through its lab bench size and footprint making it a 1-for-1 exchange with your existing lab benches

Adaptability and scalability

Quickly and easily expands to accommodate the growing needs of the lab through modular design


Eliminates human errors and unplanned downtime with complete hands-off time for staff

The Automata LINQ lab automation software enables users to create automated workflows in the visual, low-code designer.

It also automatically calculates a schedule of actions for an automated workflow. With the software, lab teams can easily run their workflow seamlessly with other laboratory activities (e.g. transferring experiment data, recording audit-related information, logging process durations and times) through a single, unified lab orchestration dashboard.

An intuitive user experience

Any team member can design and run automated workflows, with minimal training and without prior coding experience

Optimises the workflow for efficiency and/or consistency

Ensure your scheduled workflow runs with the best sequence of actions, calculated automatically

Walkaway time

Lab techs are notified of important statuses and issues in the workflow automatically, without needing to tend to the machine all day

Automata’s service team is here to help make the journey to automation as straightforward and impactful as possible.

With our team of automation experts at hand, we help your lab find the right instruments for you, run through the deployment process with ease and help ongoing support.

A partner throughout the automation process

In every interaction we are your partner, not just a provider

Optimising your automation for success

Our Project Manager and Automation Scientist will provide ongoing support while you use the Automata system

A flexible automation solution for your lab and your people

We work closely with you to understand your specific requirements

Get started on your automation journey

Is Automata right for my omics lab?

Here are a few answers to some frequently asked questions

The workcell shown is an example of a workcell capable of running a specific RNA-library preparation workflow. The exact configuration can be customised for optimal running of your workflow.

After initial reagent loading, the workcell will use the transport layer and robot arms to set up the decks as required for each of the library preparation step.

As long as the devices required are on the system then several different workflows can be deployed to each workcell.

By moving highly occupied devices such as thermal cyclers off deck it allows better utilisation of the liquid handlers to do complex liquid handling task, which in turn will increase throughput capacity for complex workflows such as library prep.

Chemistry is dependent on the instruments selected for the system so as long as your chemistry is not tied to instrumentation that is not automation friendly it can be used on this or a similar solution.

The separation of a pre-PCR and post-PCR workcell is completely dependent on your workflow. If you are using a PCR-free workflow or the physical separation isn’t needed a single system can be designed to give a similar throughput.

Yes, the liquid handlers shown in this example can be swapped out for any that are capable of performing the liquid handlers required for your chemistry.

  1. Walk-away. When benchtop automation is used for library preparation there are often still many manual touch points needed, sometimes across a multiple-day process. An operator may be required to seal and move a plate to another device in order for the process to proceed. There will also be multiple deck setups for each liquid handler. These steps are often an inconsistent time apart which leads to unnecessary downtime for scientists waiting for plate movements and manipulations.
  2. Scalability. When done manually the only way to scale library preparation methods is to get more skilled scientists to perform the process, while benchtop automation requires getting multiples of large and expensive equipment. These options aren’t efficient or viable for most laboratories and can result in more errors or suboptimal use of people and space.
  3. Utilising Current Automation. With library preparation being a workflow with high levels of automation adoption already, the next step is to integrate numerous complicated liquid handlers which LINQ can do.

Library preparation describes the process of making nucleic acid samples sequenceable. It’s the method used to prepare RNA from samples into sequencing libraries. It’s similar to DNA sequencing but has an extra step to convert the RNA to DNA.

It is commonly used in transcriptomic studies as a way to measure gene expression, which is important for understanding biological processes and disease.

Library preparation is the term used to describe the process of making a DNA/RNA/nucleic acid sample able to be sequenced. It’s a requirement for both short read and long read sequencing.

In order for a sequencer to be able to read the target DNA there has to be known specific synthetic DNA attached to the target DNA. These bits of DNA are known as sequencing adapters, and are usually supplied to the user as part of a sequencing kit. Once these are attached, the sample is part of a sequencing library. It’s call a library because it allows many different samples to be mixed and sequenced in parallel.

Depending on the application there can be other steps needed before the sequencing library is complete.

For example, the DNA may need to be made shorter and this is done by fragmentation – physically, using soundwaves, or chemically.

Some of our clients

Get in touch and find out how we can help your lab automate