Verified Workstation Application

Automated NGS Library Prep Workstation

Verified Workstation Application

Automated NGS Library Prep Workstation

Go from sample DNA to ready-to-sequence library in one automated run.

The Automated NGS Library Prep Workstation includes the OT-2 lab robot, labware, and consumables.

Full Workstation


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$29 / sample

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Next-generation sequencing (NGS) is the basis of many vitally important areas of life science, but preparing samples for sequencing is a laborious, meticulous process. The Opentrons Automated NGS Library Prep Workstation of robotics and high-quality reagents accompanied with a verified protocol, enables nearly any lab to start automating NGS library preparation end-to-end.

After placing your samples on the OT-2 lab robot, it will carry out enzymatic preparation, ligation and set up amplifications using the Temperature Module to keep your reagents cooled. Then, it will use the automated on-deck Thermocycler Module to run PCR steps and perform bead-based cleanups on the Magnetic Module.

This Opentrons workstation includes everything you need to start automating NGS library prep in your lab; the OT-2 robot with Thermocycler Module, Temperature Module, Magnetic Module, labware, Swift Bioscience library prep kit, and Omega Bio-tek magnetic beads.

This workstation can be used for the following applications:

  • Whole genome sequencing (WGS)
  • DNA sequencing
  • Metagenomic sequencing
  • Long-range PCR amplicons
  • RNA-Seq starting with full length, double stranded cDNA input
  • Detection of germline inherited SNVs and Indels
  • Copy number variation detection
  • Hybridization capture of relevant genomic regions (i.e., the exome) or transcripts of interest


  • Accuracy: 15% at 1uL

  • Precision: 5% at 1uL

  • Throughput: Fast fill a 96-well plate in 22 seconds


  • Supports Ethernet or USB connection (external dongle provided)

  • 4 USB ports available to support connection to multiple modules

  • Easy access to electronics via external PCBA enclosure

  • LED indicator provide users feedback, diagnosis & troubleshooting aid on instrument power state, system processing, ethernet, and network connectivity

User Friendly

  • Self-serve unboxing and installation

  • Reagent and bead system agnostic

  • Plug-and-play setup with access to protocol libraries to enable immediate assay implementation

  • Easily integrates to your existing instruments

  • Compatible with ANSI/SBS compliant or automation friendly tubes, microplates, deep-well plates, reservoirs and adapters


Simply load your reagents on the robot, hit 'run,' and let the workstation automate your NGS library prep from end to end.

  • 8 samples in 2hrs 50min
  • <$30 / sample for reagents + consumables
  • On-deck PCR eliminates mid-run human intervention
  • <15 minutes hands-on prep


This application has been fully tested and scientifically verified with reagent partners Swift Biosciences and Omega Bio-tek.

View our application note outlining the Swift Biosciences verification process here.

View our application note outlining the Omega Bio-tek verification process here.

Application Data

Each library constructed from 100 ng of E. coli genomic DNA resulted in an approximated yield well above the minimum required quantity for sequencing with 6% CV (coefficient of variation) across replicates in a single run. Libraries were amplified with primers specific for Illumina P5 and P7 adaptors to quantify libraries after 10 indexing PCR cycles. The constructed libraries showed an average peak fragment size of 539 bp, yielding about 34 nM per library.

figure 1

Library constructed on the OT-2 shown above shows a trace with an expected peak height of ~560 bp on the Agilent Fragment Analyzer with a High Sensitivity NGS Fragment program.

figure 2

Genome coverage remains consistent across input DNA concentrations. Libraries prepared on the OT-2 show similar or greater coverage than libraries prepared manually.



This application has been fully tested and scientifically verified with our reagent partners, Swift Biosciences and Omega Bio-tek. We recommend you use Swift 2S™ Turbo DNA Library Kit and Omega Bio-tek Mag-Bind® TotalPure NGS beads for this application. If you would like to use another kit or different beads, the OT-2 supports various reagents for DNA clean up.


This application has been verified with the Opentrons labware, including 96-well PCR plates, 2 mL tubes, 12-well reservoirs and Opentrons tips. If you have different labware requirements, reach out to our sales team to discuss modifications of this protocol to fit your needs.


We recommend using the P50 or P20 single channel pipette and P300 8-channel pipette for this application. If you have different volume requirements, contact our sales team to ask about protocol modification.

Customer spotlight

"I've done I don't know how many hundreds of minipreps in my life. I don't want to do another 3,000."
Nick Emery, DAMP of Boston University
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