Overview
NGS has revolutionized genomics research and with increased throughput demands, automation plays a crucial role in improving efficiency, accuracy, and reproducibility. As experts in NGS library preparation, we understand the importance of automation and design our products with automation in mind. Our kits include generous overages, combined reactions for simplified workflows, master mixed formulations for single reagent additions, and stable products — all of which enable the use of automation.
Our Automation Team is focused on building robust, easy-to-use methods to support our NGS library prep kits on popular third party automated liquid handling platforms. Our experts can provide consultative support for optimizing your automated workflow and develop customized solutions tailored to your lab’s needs.
Contact us today to learn more about how we can help you achieve reproducible and reliable NGS results using your automation.
Key Features and Benefits
- Generous overages to meet dead volume requirements
- Simplified workflows with fewer purifications, reagent additions, and reduced consumables
- Purpose-designed enzymes with optimized buffer formulations for NGS applications
- Library of available scripts on popular third party automation platforms
- Consultative support to optimize your automated workflow
Not seeing the full table? Rotate your phone to view in landscape mode.
| Automation Vendor | Platform | DNA Library Prep Kit with Fragmentation | DNA Library Prep Kit | mRNA Library Prep Kit | RNA Library Prep Kit with Polaris Depletion | RNA Library Prep Kit |
| Revvity* | Sciclone® G3 NGSx Workstation | ✓ | ✓ | ✓ | ✓ | R |
| Beckman Coulter | Biomek® i7 Hybrid NGS Workstation | ✓ | ✓ | D | ✓ | ✓ |
| SPT Labtech | firefly® | ✓ | ✓ | D | D | |
| Eppendorf | epMotion® 5075t | ✓ | ✓ | ✓ | ||
| Hamilton | NGS STAR™ (LSA) | ✓ | D | ✓ | ✓ | |
| NGS STAR™ (MOA) | ✓ | R | D | ✓ | ✓ | |
| Agilent | Bravo NGS Workstation | ✓ | D | |||
| Opentrons | FLEX | ✓ |
* Formerly known as PerkinElmer
✓ = Complete (successfully installed externally)
R = Ready for first external implementation
D = In development
Please reach out via our Technical Support Form if your site would be interested in being a first implementation site.
All products and platforms listed are for research use only. Not for use in diagnostic procedures.
Last updated 04-APR-2025
Questions on how to access scripts
or don’t see what you’re looking for?
Questions on how to access scripts
or don’t see what you’re looking for?
Latest Automation Update
New Scientific Poster
Evaluating a rapid automated RNA-seq workflow for ultra-low input sample types
As presented at SLAS 2025
Collaborations
VIDEOS
Sequenomics: Maximizing data quality, minimizing process complexity in NGS
Illumina DNA RNA Blood FFPE Plasma/cfDNA DNA NGS RNA NGS DNA Library Prep DNA Library Prep with Fragmentation mRNA Library Prep RNA Library Prep with Polaris DepletionThis video highlights Watchmaker’s approach to “sequenomics” — the integration of biochemistry, workflow design, and automation to enhance sequencing efficiency while reducing complexity and hands-on time.
AUTOMATION RESOURCES
Automating Watchmaker’s RNA Library Prep Kit with Polaris Depletion on the Biomek i7 Hybrid NGS Workstation
Lab Automation RNA Cell Line RNA NGS RNA Library Prep with Polaris Depletion BeckmanThis application note details the automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Biomek i7 Hybrid NGS Workstation, enabling preparation of up to 96 libraries in under 7 hours. The workflow reduces hands-on time, minimizes errors, and offers flexibility in sample processing for high-throughput RNA sequencing.
Automating Watchmaker’s high-performance next generation sequencing chemistries on the Biomek i7 liquid handler for rapid, high-throughput sample to sequence output
Metagenomic Sequencing Whole Genome Sequencing Illumina DNA Cell Line Microbial Plasma/cfDNA DNA NGS DNA Library Prep with Fragmentation BeckmanThis poster presents the integration of Watchmaker Genomics' DNA Library Prep Kit with Fragmentation into the Biomek i7 Hybrid NGS Workstation, facilitating rapid, high-throughput library preparation. The automated workflow achieves consistent, high-quality libraries with uniform insert sizes and GC coverage across various sample types and inputs, reducing human error and hands-on time.
Automated Watchmaker mRNA Library Prep Kit on Sciclone® G3 NGSx
Lab Automation RNA Cell Line RNA NGS mRNA Library Prep RevvityThis application note details the automation of the Watchmaker mRNA Library Prep Kit on the Sciclone® G3 NGSx workstation, enabling the preparation of up to 96 libraries in approximately 5 to 6 hours. The automated workflow reduces hands-on time and minimizes errors, accommodating various sample types and input amounts. The system offers flexibility in bead cleanup ratios and adapter options, enhancing reproducibility and efficiency in mRNA sequencing applications.
Modernizing DNA library preparation: An automated workflow for translational research and clinical genomics
Metagenomic Sequencing Whole Genome Sequencing Illumina DNA Cell Line Microbial Plasmid DNA NGS DNA Library Prep with Fragmentation RevvityThis poster presents an automated DNA library preparation workflow using the Watchmaker DNA Library Prep Kit with Fragmentation on the PerkinElmer Sciclone® G3 NGSx workstation. The system processes up to 96 samples per run, accommodating various inputs, including human genomic DNA, metagenomic DNA, and plasmids. The workflow reduces human error and hands-on time, with total processing for 96 samples taking approximately 3.5 to 4.5 hours. Consistent fragmentation and high sequencing uniformity across diverse GC content highlight its utility in translational and research applications.
Streamline Watchmaker’s DNA Library Prep Kit for pre-fragmented DNA on the Sciclone G3 NGSx Workstation
Lab Automation DNA Cell Line DNA NGS DNA Library Prep RevvityThis application note details the automation of the Watchmaker DNA Library Prep Kit on the Sciclone® G3 NGSx workstation, processing up to 96 samples with flexible input and cleanup options. The workflow reduces hands-on time and minimizes errors, enhancing efficiency and reproducibility in NGS applications.
Automated library preparation using Watchmaker DNA Library Prep Kit with Fragmentation on the firefly®
Lab Automation Whole Genome Sequencing DNA Cell Line DNA NGS DNA Library Prep with Fragmentation SPT LabtechThis application note outlines the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the firefly® platform, improving efficiency, reproducibility, and reducing human error in NGS workflows. The integration enables streamlined library prep for precious samples, enhancing laboratory resource utilization.
Watchmaker DNA Library Prep Kit with Fragmentation automated on the Revvity Sciclone™ G3 NGSx workstation
Lab Automation DNA Cell Line DNA NGS DNA Library Prep with Fragmentation RevvityThis application note details the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the Sciclone® G3 NGSx workstation, processing up to 96 samples per run with reduced hands-on time. The workflow supports flexible adapter options and PCR configurations, ensuring reproducible library yields and size distributions.
Automating Watchmaker DNA Library Prep Kit with Fragmentation on Biomek i7 Hybrid NGS Workstation
Lab Automation Metagenomic Sequencing Illumina DNA Cell Line Microbial Plasmid DNA NGS DNA Library Prep with Fragmentation BeckmanThis application note highlights the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the Biomek i7 Hybrid NGS Workstation, enabling high-throughput preparation of sequencing-ready libraries in under 4 hours. It emphasizes consistent library quality, uniform GC coverage, and minimized hands-on time to streamline DNA library preparation workflows.
Evaluating a simple, automatable, and sensitive solution for rapid RNA-seq
Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion RevvityThis poster showcases the automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Revvity Sciclone G3 NGSx, enabling high-quality whole transcriptome libraries from a wide range of RNA inputs. The workflow demonstrated consistent yields, no cross-contamination, and scalability up to 96 samples in under 7 hours, making it ideal for clinical and research applications. As presented at SLAS 2025.
Evaluating a rapid automated RNA-seq workflow for ultra-low input sample types
Gene Expression Analysis Lab Automation Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion HamiltonThis poster demonstrates the successful automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Hamilton Microlab® NGS STAR MOA for ultra-low input RNA samples. It shows that the automated workflow delivers high-quality, reproducible libraries comparable to manual prep, with reduced hands-on time and consistent performance across key sequencing metrics. As presented at SLAS 2025.
Automated RNA library preparation for whole transcriptome sequencing using Watchmaker Genomics’ RNA Library Prep Kit with Polaris Depletion on the epMotion 5075t workstation
Lab Automation Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion EppendorfThis application note details the development of a streamlined, automated workflow for RNA library preparation using the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Eppendorf epMotion® 5075t. The protocol demonstrates robust performance across low-input and degraded samples, enabling high-throughput, high-quality whole transcriptome sequencing with minimal hands-on time.
I don't see my automation platform listed, can you help automate my workflow?
We would be happy to explore how our Automation Team may be able to help automate your Watchmaker workflow. Please reach out to our Technical Support team to inquire about automation support on your specific platform.
Do your NGS kits include overage for automation?
Yes, all of our 96-reaction NGS prep kits include overages required for automation. Our Automation Team also designs our automation solutions to minimize required overages. For all scripts listed on our Automation Script Availability chart users will have enough overage included in the kit to split a 96-reaction kit up to four times (24-reactions/run) when running the automated workflow.
Can you share viscosity or density information of your reagents for liquid class development?
Unfortunately, we do not have specific density or viscosity information for reagents included in our NGS prep kits, however, in lieu of density or viscosity information we are happy to supply sample kits for liquid class development and optimization. Please reach out to our Technical Support team to request a sample kit for this purpose.
Do you offer large bulk formats?
We provide a variety of bulk formats, including pre-configured options and bulk packaging, which are available for purchase. We can also customize kit component volumes to meet your specific needs. We encourage you to get in touch with us so that we can discuss your specific projects and determine the ideal kit format that meets your specific needs.
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