Single Cell Automation

Automated workflows for scalable discovery

The automation advantage

Scale upMore samples, more cells, more statistical power. Your large-scale studies can deliver impressive insights, and automated workflows for Chromium assays make sure you can do it with speed and precision.
Do more with your timeAutomation lets you free up entire workdays, taking you from cell suspensions to sequencing-ready libraries for up to 96 samples, with as much as 12 hours of walkaway time.* *Walkaway times vary by automation platform and assay.
Ensure consistencyBreakthroughs depend on data you can trust, from disease biology to therapeutic development. Automation minimizes handling and improves reliability across users and samples, ensuring robust results, every time.

Magnify your impact: Proven single cell supported by automation experts

Reliable, automated cell partitioning with Chromium instruments is standard across all of our single cell assays. Beyond that, we also support automation across the rest of your workflow, with automation-ready reagents and access to our trusted network of vendors.

Ready to get started? Jump down to view specific automation workflows >

Explore automation-ready kits for 10x single cell assays

Our automation-ready reagents are specifically designed for use with liquid handling platforms and pre-optimized for required dead volumes. Workflow segments include amplification and cleanup, library construction, and 96-well multiplexing with Flex Apex (enabling throughput for up to 384 samples per week).

Count on trusted automation partners and collaborators

Our network of automation vendors includes partners who co-develop and support 10x-qualified workflows, designed to get you up and running quickly. To enable more automation options, we also work with vendors in the field to guide development of additional methods, which may be validated by 10x or supported independently by the vendor.

Choose the automation solution that best fits your needs

Access the automated protocols you need to overcome the bottlenecks in your research. This simplified overview is representative of single cell workflow stages where automation options are available, from sample processing through library construction.
Automation workflow stages

Your team of experts: 10x automation partners and collaborators

Beckman Coulter Life Sciences

Beckman Coulter Life Sciences leads in lab automation, offering liquid handlers and integrated systems for diverse applications and workflows.

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Hamilton® Robotics

Hamilton Company is a global provider of precision liquid-handling and automation technologies that power scalable, reproducible genomics workflows. © 2026 Hamilton Company. All rights reserved.

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SPT Labtech

SPT Labtech delivers compact, user-friendly liquid handling systems that streamline high-throughput genomics workflows, including NGS library prep.

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INTEGRA Biosciences

INTEGRA Biosciences offers innovative liquid handling and NGS solutions, delivering high-quality lab tools developed in Switzerland and the USA.

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Opentrons

Opentrons builds the execution layer for autonomous science with 10,000+ robots globally, accelerating intelligent, reproducible science at scale.

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Get started: Choose your assay, explore automated solutions

Don't see your favorite assay or workflow segment listed below? Want to explore closer technical collaboration for a method you have developed? Reach out to your sales specialist to discuss options and development pipelines >

10x qualified (Q): Co-developed and supported by 10x and the automation partner.

Available (A): Developed and supported independently by automation partner or collaborator. Details on method access and support are available from each vendor.

10x reviewed (R): Methods developed by the vendor where 10x Genomics has provided input for the method development and reviewed the resulting data.

In development (D): Actively being developed by automation partner or collaborator.

Beckman Coulter Life Sciences Platform: Biomek i7

Flex ApexFixation and hybridization (D)
Universal 3'3' gene expression cDNA preparation (Q) 3' gene expression library construction (Q)
Universal 5'5' gene expression cDNA preparation (Q) 5' gene expression library construction (Q) 5' TCR/BCR enrichment and library construction (A) 5' Feature Barcode library construction (A)
Epi Multiome3' gene expression cDNA preparation (Q; ATAC amplification not available) 3' gene expression library construction (Q; ATAC library construction not available)

Hamilton Robotics Platforms: Hamilton NGS STAR™ MOA NGS STARlet

Flex ApexFixation and hybridization (D with NGS STAR MOA only)
Universal 3'3' gene expression library construction (Q with NGS STAR MOA; D with NGS STARlet)
Universal 5'5' gene expression library construction (Q with NGS STAR MOA; D with NGS STARlet) 5' TCR/BCR enrichment and library construction (D)
Epi Multiome3' gene expression library construction (A; ATAC library construction not available)

SPT Labtech Platforms: firefly firefly+

Flex ApexHybridization (R) Library construction (D)
Universal 3'3' gene expression cDNA preparation (D) 3' gene expression library construction (A)
Universal 5'5' gene expression cDNA preparation (D) 5' gene expression library construction (A) 5' TCR/BCR library construction (A)
Scale BiosciencesScalePlex (D) QuantumScale (A) scMethylation (A)

INTEGRA Biosciences Platform: ASSIST PLUS

Flex ApexFFPE sample prep (A) Fixation and hybridization (A) Library construction (A)
Scale BiosciencesScalePlex (A) QuantumScale (A)

Opentrons Platform: Opentrons Flex

Universal 3'3' gene expression cDNA preparation (A) 3' gene expression library construction (A)
Universal 5'5' gene expression cDNA preparation (A) 5' gene expression library construction (A)
Scale BiosciencesscMethylation (A)

Need help choosing your automated workflow?

Speak to a sales specialist