Library prep automation

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

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.

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.

Compatible automation platforms for Illumina library preparation

See which library prep kits are automated on which liquid handling platforms, or find Illumina Qualified and/or vendor-developed methods for a given platform.

Illumina library prep products	Platforms with Illumina Qualified methods	Platforms with vendor-developed methods
AmpliSeq for Illumina AmpliSeq chemistry^a 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 LSA^a	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 MOA^a	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.

Manage workflow

Clarity LIMS

Laboratory information management system designed to track samples and manage workflows for an optimized and efficient lab. 

Prepare libraries

Illumina DNA PCR-Free Prep

High-performing, fast, and integrated PCR-free workflow for sensitive applications such as human whole-genome sequencing or tumor–normal sequencing.

Beckman Coulter Biomek i5 or Biomek i7, Hamilton NGS Star, or another compatible robotic liquid handler.

Sequence

NovaSeq X Series

Sequencing systems delivering up to 16 Tb of output, allowing sequencing of 128 human genomes at 30× coverage in a single run.

NovaSeq 6000 System

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

Analyze

Illumina DRAGEN secondary analysis

Accurate, comprehensive, and efficient secondary analysis of next-generation sequencing data.

Emedgene

A comprehensive research software platform to support tertiary analysis clinical research workflows.  

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.

Related resources

Adopt high-throughput sequencing in your lab

How to choose a LIMS for NGS

Multiplex sequencing strategies

Bioinformatics pipeline considerations

Library prep automation

Automate your library prep

Types of library prep automation protocols

Illumina Qualified

Vendor-developed

Compatible automation platforms for Illumina library preparation

AmpliSeq for Illumina

COVIDSeq Assay (96 samples)

COVIDSeq Test (RUO Version)

Illumina DNA PCR-Free Prep

Illumina DNA Prep

Illumina DNA Prep with Enrichment

Illumina RNA Prep with Enrichment

Illumina Stranded mRNA Prep

Illumina Stranded Total RNA

Nextera XT DNA

TruSight Oncology 500

TruSight Oncology 500 High-Throughput

TruSeq DNA Nano

TruSeq DNA PCR-Free

TruSeq Stranded mRNA

TruSeq Stranded Total RNA

TruSight Tumor 15

TruSight Tumor 170

Featured automation workflow: whole-genome sequencing

Manage workflow

Prepare libraries

Sequence

Analyze

Automation platform info and documentation

Related resources

Automated library prep examples

Nucleic acid QC with the Agilent Fragment Analyzer system

Automated Illumina DNA Prep metagenomics workflow

COVIDSeq workflow automation

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Library prep automation

Automate your library prep

Library Prep Automation Buyer’s Guide

Types of library prep automation protocols

Illumina Qualified

Vendor-developed

Compatible automation platforms for Illumina library preparation

Featured automation workflow: whole-genome sequencing

Manage workflow

Prepare libraries

Sequence

Analyze

Automation platform info and documentation

Related resources

Automated library prep examples

Need more info?