Library prep automation

Minimize errors, reduce hands-on-time, and enable higher throughput with automation options across Illumina library prep products

Scientist starting library prep automation sequence

Automate your library prep

Automated liquid-handling systems help labs achieve and maintain consistent results while driving efficiency. NGS library prep automation also allows for the rapid scaling of throughput while reducing hands-on time.

Illumina partners with leading vendors to provide automated protocols for Illumina library prep kits, combining our partners’ automation knowledge with our library prep and sequencing expertise to build an NGS solution that works for you.

Compatible automation platforms for Illumina library preparation

Types of library prep automation protocols

Illumina Qualified

Illumina Qualified methods are developed, tested, distributed, owned, and supported by our partners. Illumina reviews data to ensure method performance and data quality.

Vendor-developed

Vendor-developed methods are those that have been developed by an automation partner, but have not undergone data review by Illumina.

Product Brand

Illumina Qualified

Vendor-developed

AmpliSeq for Illumina

AmpliSeq chemistrya offers a highly multiplexed PCR-based workflow for a few to hundreds of targets in a single run.

  • Beckman Coulter: Biomek i5 
  • Eppendorf: epMotion 5075t 
  • Revvity: SciClone
  • Eppendorf: epMotion 5073
  • Hamilton: NGS STAR
  • Hamilton: NGS STARlet

a. 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.

COVIDSeq Assay (96 samples)

This low- to mid-throughput NGS assay enables labs of any size to identify and track the emergence and prevalence of novel SARS-CoV-2 variants.

  • Not currently available
  • Agilent: Bravo Option A
  • Beckman Coulter: Biomek i7
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: Fluent DreamPrep
COVIDSeq Test (RUO Version)

This high-throughput NGS assay enables labs to detect SARS-CoV-2 mutations to identify and track the emergence and prevalence of novel variants.

  • Not currently available
  • Agilent: Bravo Option A
  • Beckman Coulter: Biomek i7
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: Fluent DreamPrep
Illumina DNA PCR-Free Prep

An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.

  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Revvity: Zephyr
  • Tecan: DreamPrep
  • Tecan: Freedom EVO NGS
  • Beckman Coulter: Biomek i5
  • Beckman Coulter: Biomek i7
  • Not currently available
Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

  • Beckman Coulter: Biomek FXp
  • Beckman Coulter: Biomek iSeries
  • Beckman Coulter: NGeniuS
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: Freedom EVO NGS
  • Tecan: DreamPrep
  • Agilent: Bravo Option A
  • Agilent: Bravo Option B
Illumina DNA Prep with Enrichment

A fast, integrated workflow that provides sequencing-ready DNA libraries for a wide range of targeted sequencing applications.

  • Beckman Coulter: Biomek iSeries
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: Freedom EVO NGS
  • Agilent: Bravo Option A
  • Agilent: Bravo Option B
  • Beckman Coulter: Biomek FXp
Illumina RNA Prep with Enrichment

A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.

  • Beckman Coulter: Biomek i7
  • Eppendorf: epMotion 5075t
  • Revvity: SciClone
  • Agilent: Bravo Option A
  • Hamilton: NGS STAR
Illumina Stranded mRNA Prep

A rapid, cost-effective workflow for accurate, unbiased detection of the protein-coding transcriptome with precise measurement of strand information.

  • Beckman Coulter: Biomek i7
  • Eppendorf: epMotion 5075t
  • Revvity: SciClone
  • Hamilton: NGS STAR
Illumina Stranded Total RNA

Streamlined RNA-Seq solution for clear and comprehensive analysis across the coding and noncoding transcriptome with exceptional study flexibility. 

  • Beckman Coulter: Biomek i7
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: DreamPrep
Nextera XT DNA

A 90-min workflow to prepare DNA libraries for small genomes, PCR amplicons, plasmids, and cDNA sequencing, with a low DNA input requirement.

  • Beckman Coulter: Biomek FXp
  • Beckman Coulter: Biomek iSeries
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: SciClone
  • Tecan: Freedom EVO NGS
  • Agilent: Bravo Option B
TruSight Oncology 500

Assay enabling comprehensive genomic profiling with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD*) from FFPE tissue.

*HRD is only available with the addition of the TruSight Oncology 500 HRD kit to TruSight Oncology 500. Not available in Japan.

  • Beckman Coulter: Biomek NXp
  • Beckman Coulter: Biomek i7
  • Hamilton: NGS STAR/SBS STAR LSAa
  • Beckman Coulter: Biomek i5
  • Hamilton: NGS STARlet
  • Revvity: Sciclone

a. As of January 2022, Hamilton renamed the NGS STAR configuration for TruSight Oncology 500 library prep to SBS STAR LSA. All existing Illumina Qualified methods are backwards compatible and will continue to run on this system.

TruSight Oncology 500 High-Throughput

Assay enabling comprehensive genomic profiling with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI) from FFPE tissue, with added scalability.

  • Beckman Coulter Biomek i7
  • Hamilton NGS STAR with 96 MPH/SBS STAR MOAa
  • Not currently available

a. As of January 2022, Hamilton renamed the NGS STAR configuration for TruSight Oncology 500 High-Throughput library prep to SBS STAR LSA. All existing Illumina Qualified methods are backwards compatible and will continue to run on this system.

TruSeq DNA Nano

Generate whole-genome sequencing libraries and efficiently interrogate samples with limited available DNA.

  • Beckman Coulter: Biomek FXp
  • Beckman Coulter: Biomek iSeries
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: Sciclone NGS and NGSx
  • Tecan: Freedom EVO NGS
  • Agilent: Bravo Option B
TruSeq DNA PCR-Free

Simple, all-inclusive whole-genome sequencing (WGS) library preparation that provides accurate and comprehensive coverage of complex genomes.

  • Beckman: Coulter Biomek FXp
  • Eppendorf: epMotion 5075t
  • Revvity: Scicione NGS and NGSx
  • Agilent: Bravo Option B
  • Hamilton: NGS STAR
  • Tecan: Freedom EVO NGS
TruSeq Stranded mRNA

Prepare sequencing libraries from mRNA to get a clear view of the coding transcriptome with strand-specific information.

  • Beckman Coulter: Biomek FXp
  • Beckman Coulter: Biomek iSeries
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: Sciclone NGS and NGSx
  • Tecan: Freedom EVO NGS
  • Agilent: Bravo Option A
  • Agilent: Bravo Option B
TruSeq Stranded Total RNA

A robust, highly scalable whole-transcriptome analysis (RNA-Seq) solution for various species and sample types, including human, mouse, and formalin-fixed, paraffin-embedded (FFPE) tissue.

  • Beckman Coulter: Biomek FXp
  • Eppendorf: epMotion 5075t
  • Hamilton: NGS STAR
  • Revvity: Sciclone NGS and NGSx
  • Tecan: Freedom EVO NGS
  • Agilent: Bravo Option B
TruSight Tumor 15

Focused NGS panel to assess 15 commonly mutated genes in solid tumors with a simple and rapid workflow.

  • Beckman Coulter: Biomek 4000
  • Eppendorf: epMotion 5075t
  • Revvity: Zephyr
  • Not currently available
TruSight Tumor 170

Comprehensive NGS assay targeting 170 genes associated with solid tumors.

  • Beckman Coulter: Biomek NXp
  • Hamilton: NGS STAR
  • Not currently available

Featured automation workflow: whole-genome sequencing

Track samples, manage your runs, and launch into production with preset laboratory information management system (LIMS) protocols. Leverage a compatible robotic liquid handler to prepare libraries for rapid high-throughput sequencing and data analysis.

1
Manage
2
Prep
3
Sequence
4
Analyze

Automation platform info and documentation

Learn more about the automated liquid-handling platforms offered by Illumina partners. View partner documentation to learn how to automate a specific Illumina library prep kit.

Automated library prep examples

COVIDSeq workflow automation

COVIDSeq Assay and COVIDSeq Test workflows are compatible with a range of automation solutions and configurable for batch sizes from 8–96 samples.

Need more info?

Contact us to learn more about automation partners and Illumina Qualified methods.