Methods for library prep automation

High-Throughput Library Prep Automation

Automating the Library Prep Workflow

Automating sequencing library preparation minimizes errors, reduces hands-on time, and enables higher throughput. Illumina facilitates kit automation by partnering with leading automation vendors in liquid handling, fragmentation, and size selection. The resulting solutions, described below, significantly decrease the time and expense of method development and optimization.

Automated Liquid Handling

Liquid-handling robots are important tools for labs seeking to increase throughput and consistency. These systems reduce hands-on time and can be programmed for various lab needs, making them ideal for labs that require high flexibility. Illumina library prep kits can be automated on most general-purpose liquid-handling robots.

Various leading vendors have developed methods for Illumina kits. These automated methods eliminate the time and effort associated with developing a method. The “Illumina Qualified” designation means our analysis has shown libraries prepared with these methods perform comparably to those prepared manually.

Select a logo below to display available automated methods for that vendor:

Automated Library Prep Buyer's Guide

Learn what to consider when evaluating library prep automation systems.

Read Guide
Agilent Technologies
Beckman Coulter
Eppendorf
Hamilton Robotics
Perkin Elmer
Tecan
Agilent Technologies

Science for Life Laboratories is working with Illumina to develop methods for various Library Prep workflows. Methods and associated documentation are available on GitHub.

Website GitHub Repository

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
Nextera DNA Flex Other   Bravo Option B
TruSeq Stranded Total RNA Other   Bravo Option B
TruSeq RNA Exome Other   Bravo Option B
TruSeq Nano DNA Other   Bravo Option B
Nextera XT DNA Other   Bravo Option B
Nextera DNA Exome Other   Bravo Option B
TruSeq Stranded mRNA Other   Bravo Option B
TruSeq DNA PCR-Free Other   Bravo Option B

Beckman Coulter

*In order to accommodate for higher dead volume requirements associated with automated platforms and variation in overfill volumes by the original reagent manufacturer, more than one AmpliSeq for Illumina kit may be required when preparing the maximum number of libraries per kit.

Biomek Liquid Handlers –Robust systems that offer superior flexibility for low to high throughput automated library preparation. Industry leading software enables the creation of easy to use, pre-programmed solutions to address the essential steps of library construction, DNA purification and size selection as well as qPCR setup, normalization and pooling. For high throughput processing, the Biomek FXP Dual Multi- 96 and Span 8 system maximizes throughput and efficiency with combined whole plate and individual well processing on a single system.

Website Phone: 1-800-732-2345

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
AmpliSeq for Illumina* Vendor Biomek i5
Nextera DNA Flex Vendor Biomek FXp, Biomek iSeries
TruSight Tumor 170 Vendor Biomek NXp
TruSight Tumor 15 Vendor Biomek 4000
TruSight Cancer/TruSight Enrichment Vendor Biomek 4000
Nextera Rapid Capture Custom Enrichment Vendor Biomek 4000
TruSeq DNA Exome Vendor   Biomek FXp
Nextera DNA Exome Vendor   Biomek FXp
TruSeq RNA Exome Vendor Biomek FXp, Biomek iSeries
Nextera XT DNA Vendor Biomek FXp, Biomek iSeries
TruSeq Nano DNA Vendor Biomek FXp, Biomek iSeries
TruSeq DNA PCR-Free Vendor Biomek FXp
TruSeq Stranded Total RNA Vendor Biomek FXp
TruSeq Stranded mRNA Vendor Biomek FXp, Biomek iSeries
TruSeq RNA v2 Vendor   Biomek FXp

Eppendorf


*In order to accommodate for higher dead volume requirements associated with automated platforms and variation in overfill volumes by the original reagent manufacturer, more than one AmpliSeq for Illumina kit may be required when preparing the maximum number of libraries per kit.

The Eppendorf epMotion product family of automated pipetting systems are well known for accuracy, reproducibility and their ease of use. A variety of options like gripper transport, vacuum station, integrated mixer, temperature control of plates etc., optimize the epMotion system for laboratory routine tasks such as library preparation, PCR set-up, DNA/RNA purification, bead assays or even cell handling.

Website Email Contact

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
AmpliSeq for Illumina* Vendor epMotion 5075t
Nextera DNA Flex Vendor epMotion 5075t
Nextera XT DNA Vendor epMotion 5075t
TruSight RNA Pan Cancer Vendor epMotion 5075t
TruSight RNA Fusion Vendor epMotion 5075t
TruSight Tumor 15 Vendor epMotion 5075t
TruSight Cancer/TruSight Enrichment Vendor epMotion 5075t
Nextera Rapid Capture Custom Enrichment Vendor epMotion 5075t
Nextera DNA Exome Vendor epMotion 5075t
TruSeq RNA Exome Vendor epMotion 5075t
TruSeq Nano DNA Vendor epMotion 5075t
TruSeq Stranded Total RNA Vendor epMotion 5075t
TruSeq Stranded mRNA Vendor epMotion 5075t
TruSeq DNA PCR-Free Vendor epMotion 5075t

Hamilton Robotics

A leader in liquid handling equipment and laboratory automation technology, Hamilton Robotics is known for advancing life science and biotechnology through reliability, performance and flexibility. Hamilton has partnered with Illumina to develop standard library prep automation solutions. Hamilton's platforms include Microlab ® NIMBUS , the first in its class of compact, high-speed, personalized pipetting workstations; Microlab STAR , Hamilton's highest selling automated pipetting platform; and Hamilton VANTAGE , its newest vertically-integrated liquid handler.

Website Email Phone: 1-800-648-5950

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
Nextera DNA Flex Vendor NGS STAR
TruSeq DNA Exome Vendor   NGS STAR
Nextera DNA Exome Vendor   NGS STAR
Nextera Rapid Capture Custom Enrichment Vendor   NGS STAR
TruSight Cancer/TruSight Enrichment Vendor   NGS STAR
TruSight Tumor 170 Vendor NGS STAR
TruSeq RNA Exome Vendor NGS STAR
TruSeq Nano DNA Vendor NGS STAR
TruSeq Stranded Total RNA Vendor NGS STAR
TruSeq Stranded mRNA Vendor NGS STAR
TruSeq DNA PCR-Free Vendor     NGS STAR
Nextera XT DNA Vendor NGS STAR
16S rRNA Vendor NGS STAR

PerkinElmer

*In order to accommodate for higher dead volume requirements associated with automated platforms and variation in overfill volumes by the original reagent manufacturer, more than one AmpliSeq for Illumina kit may be required when preparing the maximum number of libraries per kit.

PerkinElmer's library prep automation solutions eliminate the processing bottlenecks presented by today's sequencing technologies. Our automation and microfluidics platforms enable scientists to process samples start to finish in a user-friendly, easy-to-implement manner. Standardized hardware configurations with pre-validated protocols and instrumentation to measure the fundamental characteristics of nucleic acid samples, provide the needed flexibility and quality control for dynamically changing applications and sample prep chemistries. PerkinElmer's library prep instrument is fully supported by a dedicated and knowledgeable applications team that provides full instrument training and on-going support.

Website Email

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
AmpliSeq for Illumina* Vendor Sciclone
Nextera DNA Flex Vendor Sciclone
TruSight Tumor 15 Vendor Zephyr
TruSight Cancer/TruSight Enrichment Vendor Zephyr
Nextera Rapid Capture Custom Enrichment Vendor Zephyr
TruSeq DNA Exome Vendor     Sciclone
TruSeq RNA Exome Vendor Sciclone NGS and NGSx
TruSeq Nano DNA Vendor Sciclone NGS and NGSx
TruSeq DNA PCR-Free Vendor Sciclone NGS and NGSx
TruSeq Stranded Total RNA Vendor Sciclone NGS and NGSx
TruSeq Stranded mRNA Vendor Sciclone NGS and NGSx
TruSeq RNA v2 Vendor   Sciclone NGS and NGSx
Nextera XT DNA Vendor Sciclone

Tecan

The Tecan Freedom EVO ® platform offers the most flexible pipetting platform available today, providing you with the tools you need to automate your laboratory research. In addition, we provide numerous standardized packages for specific applications, including sequencing library preparation.

Website Email

Available Automated Methods Liquid Handling Platforms
Kit Source Illumina Qualified Docs  
TruSeq RNA Exome Vendor Freedom EVO NGS
TruSeq Nano DNA Vendor Freedom EVO NGS
TruSeq Stranded mRNA Vendor Freedom EVO NGS
TruSeq Stranded Total RNA Vendor Freedom EVO NGS
TruSeq DNA PCR-Free Vendor Freedom EVO NGS
Nextera XT DNA Vendor Freedom EVO NGS

While we make every effort to keep this list up-to-date, please contact vendors for the latest details.
Note: All trademarks are the property of their respective owners.

Fragmentation and size selection can be laborious and time-consuming. Advanced Analytical, Covaris, PerkinElmer, and Sage offer solutions that make it easier for our customers to automate these steps. Our user guides also include recommended instrument settings for Covaris shearing systems.

Read more below to learn about different library prep automation solutions provided by these companies.

Available Library Prep Automation Methods
Advanced Analytical
Fragment Analyzer: Quantification and qualification of NGS libraries, genomic DNA and RNA
  • 2014 Frost & Sullivan New Product Innovation Award
  • Automation: Analyze up to 288 samples unattended in batches of 12 or 96 samples
  • High Sensitivity: Detect peaks below 5 pg/µl and smears as low as 50 pg/µl
  • Wide Sizing Range: Analyze DNA from 10 bp through 40,000 bp
  • Dependable Operation: Quick set up, fast run times, negligible failure rates
  • Illumina tested workflows
Learn More
Covaris
Covaris M220: Library prep made easy – “click and shear” in single-sample format
  • Fast: Ready to process samples in less than 2 minutes
  • Easy: Intuitive operation, no training needed
  • Cool: Integrated temperature control, no ice or external chiller needed
  • Versatile: Select fragment distributions between 150 bp to 5 kb
  • Quiet: Can be used anywhere in the lab
Learn More
Covaris
Covaris S220: Versatile DNA shearing in a single-sample format
  • The S220 Focused-ultrasonicator is a versatile, high-power system engineered for DNA shearing and other pre-analytical sample processing applications
  • S220 delivers controlled energy precisely and accurately to sample volumes from 25 µl to 10 ml in single-sample format
Learn More
Covaris
Covaris E220: Multi-sample DNA shearing in a batch-processing format
  • The E220 Focused-ultrasonicator enables multi-sample, batch preparation, processing a wide range of sample types and volumes, fragmenting 1 to 96 samples in a single batch
Learn More
High-Throughput Genomics for Disease Research

High-throughput genomic studies with tens to hundreds of thousands of samples require fast, cost-effective tools. We offer array and NGS technologies with sample-to-analysis solutions and collaborative expertise to meet these needs.

Learn More
High-Throughput Genomics for Disease Research
Perkin Elmer
LabChip GX Touch: Quantification and integrity assessment of NGS libraries, genomic DNA, and RNA
  • Automation: Unattended analysis of up to 384 samples
  • Flexibility: Cherry pick sample wells directly from 96 or 384 well plates
  • Rapid Analytics: Sample data generated in as few as 30 seconds per well
  • Sample Integrity Metrics: Automated sample quality scoring for both RNA and gDNA
  • Economical Sample Requirements: Use only 2 µl sample per analysis
  • Comprehensive Assay Selection: Choose from standard DNA or RNA, high sensitivity DNA, genomic DNA, and pico RNA
Learn More
Perkin Elmer
LabChip XT: Automated DNA size selection
  • Fast, reproducible, high resolution sizing of DNA, < 30 minute processing
  • Quantitative, digital data
  • Dry electrode contact and independent channels minimize potential for cross contamination
  • Ability to recollect non-fractionated sample and collect multiple fractions per sample
Learn More
Sage Science
Pippin Prep and BluePippin: Automated DNA size selection
  • Eliminate variability and time spent on manual gels with a cost-effective, load-and-go automated size selection system that delivers high yields
  • Fractionate up to 5 samples per run and collect targets from 50 bases to 1.5 Kb with Pippin Prep, and up to 50 Kb for mate pair libraries with BluePippin
  • Improve your genome assembly quality with more reliable, precise sizing information
Learn More
Interested in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email address.
Multiplex Sequencing
Multiplex Sequencing

Pool and sequence large numbers of libraries during a single sequencing run.

Learn More
Latest Genome Sequencer
Explore the NovaSeq Series

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Learn More

The NeoPrep System has been discontinued. Alternative automation solutions are shown above. Illumina remains committed to providing you with high-quality support and service.