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

Methods are developed by our automation partners with input from Illumina. Illumina reviews sequencing data from these methods to ensure performance and data quality. Our partners own, supply, install, and support these methods. Our partners service and support their liquid handler systems.

Illumina Qualified Plus

Illumina co-develops and tests the method with our automation partners. Our partners own, supply, and install these methods. Illumina provides front-line field and technical support for these methods.* Our partners provide secondary support for these methods. Our partners service and support their liquid handler systems.

Partner-developed

These methods are developed and tested by our automation partners. Illumina does not review the data from these methods. Our partners own, install, and support these methods. Our partners service and support their liquid handler systems.

*Support levels may vary by region. Contact your local support team for more information.

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 partner-developed methods for a given platform.

Illumina Qualified

Illumina Qualified Plus

	Beckman Coulter	Eppendorf	Hamilton	Revvity	Tecan
AmpliSeq for Illumina**	Biomek i5	epMotion 5075t epMotion 5073	NGS STAR NGS STARlet	Sciclone G3 NGSx
AmpliSeq for Illumina Cancer HotSpot Panel v2**	Biomek i5 Biomek NGeniuS	epMotion 5075t epMotion 5073		Sciclone G3 NGSx
AmpliSeq for Illumina Comprehensive Panel v3**	Biomek i5
AmpliSeq for Illumina Focus Panel**	Biomek i5	epMotion 5075t epMotion 5073		Sciclone G3 NGSx
COVIDSeq Assay (96 samples)	Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	Fluent DreamPrep
COVIDSeq Test (RUO Version)		epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	Fluent DreamPrep
Illumina Complete Long Read Prep, Human		epMotion 5075t		Sciclone G3 NGSx
Illumina DNA PCR-Free Prep	Biomek i5 Biomek i7 Biomek NGeniuS	epMotion 5075t	NGS STAR NGS STARlet	Fontus NGS Sciclone G3 NGSx Sciclone G3 NGSx iQ	DreamPrep
Illumina DNA Prep	Biomek i5 Biomek i7 Biomek NGeniuS	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	DreamPrep Freedom EVO NGS
Illumina DNA Prep with Exome 2.0 Plus Enrichment	Biomek i7	epMotion 5075t	NGS STAR NGS STARlet	Sciclone G3 NGSx Sciclone G3 NGSx iQ	DreamPrep
Illumina DNA Prep with Exome 2.5 Enrichment		epMotion 5075t	NGS STAR NGS STARlet	Sciclone G3 NGSx Sciclone G3 NGSx iQ
Illumina RNA Prep with Enrichment	Biomek i5 Biomek i7 Biomek NGeniuS	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ	DreamPrep
Illumina Stranded mRNA Prep	Biomek i7	epMotion 5075t	STAR MOA	Sciclone G3 NGSx Sciclone G3 NGSx iQ	DreamPrep
llumina Stranded Total RNA Prep		epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ	DreamPrep
Nextera XT DNA	Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	DreamPrep
Pillar Biosciences oncoReveal Solid Tumor v2 Gene Panel Kit	Biomek NGeniuS
TruSeq DNA Nano	Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx	Freedom EVO NGS
TruSeq DNA PCR-Free	Biomek i5 Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ	Freedom EVO NGS DreamPrep
TruSeq Stranded mRNA	Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	Freedom EVO NGS
TruSeq Stranded Total RNA	Biomek i7	epMotion 5075t	NGS STAR	Sciclone G3 NGSx Sciclone G3 NGSx iQ Zephyr G3 NGS	Freedom EVO NGS DreamPrep
TruSight Oncology 500	Biomek i5 Biomek i7 Biomek NGeniuS	epMotion 5075t	NGS STAR NGS STARlet	Fontus NGS Sciclone G3 NGSx	DreamPrep
TruSight Oncology 500 ctDNA v2			STAR MOA
TruSight Oncology 500 (DNA Only)	Biomek i5 Biomek i7 Biomek NGeniuS
TruSight Oncology 500 High-Throughput	Biomek i7		STAR MOA		DreamPrep
TruSight RNA Pan-Cancer Panel	Biomek i7	epMotion 5075t
TruSight Tumor 15		epMotion 5075t
TruSight Tumor 170	Biomek i5		NGS STAR NGS STARlet

Starting in January 2022, Hamilton will refer to the NGS STAR configuration for TruSight Oncology library preparations as the SBS STAR (LSA). All existing Illumina Qualified methods are backwards compatible and will continue to run on this system as this change is in name only.

** 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.

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

Automated library prep examples

Nucleic acid QC with the Agilent Fragment Analyzer system

The Fragment Analyzer system accurately assesses quality and quantity of isolated nucleic acids and prepared libraries to optimize cluster generation during sequencing.

Automated Illumina DNA Prep metagenomics workflow

This streamlined automated workflow generates highly uniform libraries and provides excellent data for species identification, metagenomic profiling, and de novo genome assembly.

COVIDSeq workflow automation

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

Automation workflow for Illumina DNA Prep with Exome 2.5 Enrichment

This workflow automates library preparation and enrichment on the Hamilton SBS STARlet Automated Liquid Handling Platform with consistent, high-quality data with less hands-on time, compared to the manual workflow.

For every lab, everywhere

Illumina Single Cell 3' RNA Prep

NGS Workflow Finder

Multiomic data analysis for any lab

Illumina Proactive Instrument Performance Service

Do more, faster than ever

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Illumina innovation roadmap

Illumina innovation roadmap

Illumina innovation roadmap

Illumina innovation roadmap

Illumina innovation roadmap

Illumina innovation roadmap

Illumina innovation roadmap

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

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For every lab, everywhere

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For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

Library prep automation

Automate your library prep

Library Prep Automation Buyer’s Guide

Types of library prep automation protocols

Illumina Qualified

Illumina Qualified Plus

Partner-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

Nucleic acid QC with the Agilent Fragment Analyzer system