Introduction to Sequencing 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.
Available Automated Methods
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.
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.
| 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 | |
| TruSight Oncology 500 | Vendor | ● | ● | Biomek NXp |
| TruSight Oncology 500 | Vendor | ● | Biomek i5 | |
| Nextera Flex for Enrichment | Vendor | ● | Biomek FXp | |
| 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 |
| 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.
| Available Automated Methods | Liquid Handling Platforms | |||
|---|---|---|---|---|
| Kit | Source | Illumina Qualified | Docs | |
| Nextera Flex for Enrichment | Vendor | ● | ● | epMotion 5075t |
| 16S rRNA | Vendor | ● | epMotion 5075t, epMotion 5073 | |
| AmpliSeq for Illumina* | Vendor | ● | ● | epMotion 5075t |
| AmpliSeq for Illumina* | Vendor | ● | epMotion 5073 | |
| 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 |
| 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.
| Available Automated Methods | Liquid Handling Platforms | |||
|---|---|---|---|---|
| Kit | Source | Illumina Qualified | Docs | |
| TruSight Oncology 500 | Vendor | ● | ● | NGS STAR |
| AmpliSeq for Illumina* | Vendor | ● | NGS STAR, NGS STARlet | |
| Nextera Flex Enrichment | Vendor | ● | ● | NGS STAR |
| Nextera DNA Flex | 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.
| Available Automated Methods | Liquid Handling Platforms | |||
|---|---|---|---|---|
| Kit | Source | Illumina Qualified | Docs | |
| Nextera Flex Enrichment | Vendor | ● | Sciclone | |
| AmpliSeq for Illumina* | Vendor | ● | ● | Sciclone |
| Nextera DNA Flex | Vendor | ● | ● | Sciclone |
| TruSight Tumor 15 | Vendor | ● | ● | Zephyr |
| 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.
| Available Automated Methods | Liquid Handling Platforms | |||
|---|---|---|---|---|
| Kit | Source | Illumina Qualified | Docs | |
| Nextera DNA Flex | Vendor | ● | Freedom EVO NGS | |
| Nextera Flex Enrichment | Vendor | ● | Freedom EVO NGS | |
| 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.
Library Prep Technical Tips
Quantification and Quality Control
Find out how to quantify and validate final libraries for a successful sequencing run.
Read Technical BulletinDNA/RNA Isolation Considerations
Find guidance to help you avoid contamination while purifying DNA/RNA before library preparation.
Read Technical BulletindsDNA Library Concentration
Learn how to convert library concentration from ng/µl to nM for some Illumia library preparation methods.
Read Technical BulletinAutomated Fragmentation and Size Selection
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.
Fragment Analyzer: Quantification and qualification of NGS libraries, genomic DNA and RNA
- Versatile: Choose from over 20 kits to QC DNA samples from 35 – 60,000 bp and RNA samples from 15 – 6,000 nt
- High Performance: Accurate quantification of peaks to 5 pg/µL and smears to 50 pg/µL with up to 3 bp resolution
- Variable Throughput: Analyze up to 288 samples unattended in batches of 12, 48, or 96
- Flexible: Streamline analysis of multiple sample types with always accessible drawers and two gel input lines
- API Control: Robotic integration enables continuous automated analysis of over 2,400 samples per day
- Illumina tested workflows
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
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
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
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
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
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
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
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Related Solutions
Multiplex Sequencing
Pool and sequence large numbers of libraries during a single sequencing run.
Explore the NovaSeq Series
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
The NeoPrep System has been discontinued. Alternative automation solutions are shown above. Illumina remains committed to providing you with high-quality support and service.