Library Preparation
DNA Sequencing RNA Sequencing Methylation Sequencing Library Preparation High-Throughput Sequencing

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.

Accelerate your NGS workflow with Illumina-ready automation

Integrated workflows

Illumina offers components for every stage of the next-generation sequencing (NGS) process—from library prep and automation protocols to sequencing, data analysis, and support.

Flexible throughput options

Configure automation setups to meet a range of sample volumes and workflow needs.

Access to Illumina-ready protocols

Use protocols developed and qualified in collaboration with automation partners alongside Illumina library prep kits.

Comprehensive support

Get help with setup, training, and ongoing technical support.

Library Prep Automation Buyer’s Guide

This guide walks you through the range of automation tools available for NGS library prep and helps you find a solution tailored for your application, throughput, and budget needs. Learn about top considerations for building your automated library prep protocol.

Featured Illumina-ready protocols

TruSight Oncology 500 v2

High-throughput prep for up to 96 DNA or 48 DNA and 48 RNA libraries with over 50% less hands-on time. Compatible with Hamilton Microlab NGS STAR MOA and Beckman Biomek i7 systems.

Illumina TruSight Oncology 500 ctDNA v2

Process up to 48 DNA libraries with over 65% less hands-on time compared to manual methods. Compatible with Hamilton Microlab NGS STAR MOA and Beckman Biomek i7 systems.

Flexible automation, the way you need it

Choose between Illumina-ready, end-to-end support or flexible partner-developed solutions—both designed to streamline NGS library prep from DNA to results.

Full Illumina-ready automation support

Best for teams that want Illumina-ready protocols and direct Illumina support.

  • Validated protocols
    Co-developed and qualified with Illumina
  • Confidence in training
    Illumina-led onboarding for your team
  • Production-ready
    Illumina assists with performance qualification
  • Direct support
    Illumina is your main technical contact
  • Hardware-backed
    Automation partners service their systems

Illumina partner network

Best for teams that want flexibility with partner-developed workflows, with Illumina as backup.

  • Partner-developed protocols

    Certified by Illumina if assay metrics are met
  • Partner-managed support
    Install, service, and maintain systems
  • Field expertise
    Partners provide training and performance qualification
  • Illumina backup
    Secondary support for chemistry when needed
  • Flexibility
    Broader choice of platforms and providers

All Illumina partner network automation protocols

Explore which library prep kits are automated across partner-developed liquid handling platforms.

  Beckman Coulter Eppendorf Hamilton Revvity Tecan SPT Labtech
Whole Genome Sequencing
Illumina DNA Prep Biomek i7
Biomek NGeniuS 		epMotion 5075t NGS STAR Sciclone G3 NGSx DreamPrep Firefly
Illumina DNA PCR-Free Prep Biomek i7
Biomek NGeniuS 		epMotion 5075t NGS STAR Sciclone G3 NGSx DreamPrep  
Nextera XT DNA Library Preparation Kit Biomek i7 epMotion 5075t NGS STAR Sciclone G3 NGSx    
TruSeq DNA PCR-Free Biomek i5
Biomek i7 		epMotion 5075t   Sciclone G3 NGSx Freedom Evo NGS  
TruSeq DNA Nano Biomek i7 epMotion 5075t NGS STAR   Freedom Evo NGS  
Targeted Sequencing
AmpliSeq for Illumina Cancer Hotspot Panel v2* Biomek i5 epMotion 5075t
epMotion 5074 		       
Illumina DNA Prep with Enrichment Biomek i7 epMotion 5075t NGS STAR Sciclone G3 NGSx    
Illumina DNA Prep with Exome 2.5 Enrichment   epMotion 5075t NGS STARlet Sciclone G3 NGSx
Sciclone G3 NGSx iQ 		   
Pillar Biosciences oncoReveal Solid Tumor v2 Panel Biomek NGeniuS          
TruSight Tumor 15   epMotion 5075t        
  Beckman Coulter Eppendorf Hamilton Revvity Tecan SPT Labtech
Whole Transcriptome Sequencing
llumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus   epMotion 5075t NGS STAR Sciclone G3 NGSx    
TruSeq Stranded Total RNA Biomek i7 epMotion 5075t NGS STAR Sciclone G3 NGSx Freedom Evo NGS  
Targeted Sequencing
Illumina DNA Prep with Enrichment Biomek i7
Biomek NGeniuS 		epMotion 5075t   Sciclone G3 NGSx    
COVIDSeq Assay (96 samples)       Sciclone G3 NGSx    
COVIDSeq Test (RUO Version)       Sciclone G3 NGSx    
TruSight RNA Pan-Cancer Panel Biomek i7          
mRNA Sequencing
Illumina Stranded mRNA Prep Biomek i7 epMotion 5075t   Sciclone G3 NGSx    
TruSeq Stranded mRNA Biomek i7 epMotion 5075t NGS STAR Sciclone G3 NGSx Freedom Evo NGS  
  Beckman Coulter Eppendorf Hamilton Revvity Tecan SPT Labtech
AmpliSeq for Illumina Comprehensive Panel v3* Biomek i5          
AmpliSeq for Illumina Focus Panel* Biomek i5 epMotion 5075t
epMotion 5074 		       
TruSight Tumor 170 Biomek i5   NGS STAR      

* 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.

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.

SPT Labtech

Beckman Coulter

Eppendorf

Hamilton

Revvity

Tecan

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

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.

Need more info?

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