NeoPrep FAQs

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  • General

  • The NeoPrep System has a touch screen monitor with on-screen keyboard to enable on-instrument configuration and setup using the software interface. A mouse and/or keyboard can be connected via the external USB ports if preferred. The system can also be customized to disable the on-screen keyboard and only use an external keyboard; however, these are not provided with the system. 

  • Libraries

  • Library concentrations are reported on the NeoPrep Control Software screen after the run is complete. In addition, the final report can be accessed using the Access Logs function on the Welcome Screen. The run report can also be saved to a network drive by specifying an alternate output folder location on the System Configuration screen. The information is also streamed to BaseSpace Sequence Hub if run was set-up in BaseSpace Sequence Hub Prep tab.

    The complete NeoPrep protocol results in 10 µl 10 nM library after the library droplet is collected from the library card, diluted in RSB, and separated from the oil.

  • Reagents

  • To perform a run on the NeoPrep System, a single-use NeoPrep System library prep kit is required. Each kit contains the following for a single run:

    • Assay specific reagent plate and guide affixed on the reagent plate
    • Assay specific reagent tubes
    • Oil vial and funnel
    • Library card
    • Library card guide
    • Library separation tube strips

    For specific library prep kit contents and storage conditions, see the appropriate library prep reference guide.

    The used library card contains hazardous materials. Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Wear protective equipment, including eye protection, gloves, and a laboratory coat. Handle the used library card as chemical waste. Dispose of it in accordance with the governmental safety standards for your region. Refer to the safety data sheets (SDSs) for the consumables in the kit that you are using for detailed environmental, health, and safety information and dispose of according to your institution and other requirements. SDSs are available on the Illumina website at

    Guaranteed shelf life is three months from date of shipment.

  • Workflow

  • Up to 16 libraries can be prepared. If you run less than 16 libraries, Illumina recommends that the wells that do not have samples are the last ones in the row. RSB should be loaded into empty sample wells.

    A sample sheet can be loaded during the Load Library Card step. If you are not using the default index adapter layout, create and edit a sample sheet to record information about your samples and indexes. Illumina recommends that you use IEM to create an appropriate sample sheet. For more information, see the Illumina Experiment Manager Software Guide.

    Use the following required pipettes and tips. Other pipettes and tips are not supported and can result in reagents not dispensing properly and run failure.

    20 μl Volume:

    • Pipet-Lite XLS+ 8-channel LTS, 2 μl to 20 μl—Rainin, catalog # L8-20XLS+
    • One of the following 20 µl tips:
      • LTS tips 20 µl. Presterilized. Filter—Rainin, catalog # RT‑L10F
      • ART Barrier Pipette Tips 20 µl; 20 µl SoftFit-L—Fisher Scientific, catalog # 2749RI

    200 μl Volume:

    • Pipet-Lite XLS+ 8-channel LTS, 20 μl to 200 μl—Rainin, catalog # L8-200XLS+
    • One of the following 200 µl tips:
      • LTS tips 200 µl. Presterilized. Filter—Rainin, catalog # RT‑L200F
      • ART Barrier Pipette Tips 200 µl; 200 µl SoftFit-L—Fisher Scientific, catalog # 2769RI

    Yes, you can select three types of workflows on the NeoPrep System:

    • library prep only
    • library prep and quantification
    • library prep, quantification, and normalization

    If you are not using the on-board quantification, libraries can be quantified using a fluorometric quantification method that uses dsDNA binding dyes or qPCR. For more information, see the appropriate library prep reference guide.

    A blue dye is used in NeoPrep library prep reagents to aid in loading and collection. It appears as a characteristic peak at 200–250 bp in a Bioanalyzer trace and is not indicative of issues with the final library. The blue dye has no impact on downstream sequencing.

    Fragment Analyzer does not show the blue dye peak in the trace due to dilution on that instrument.

    NeoPrep libraries are ready for cluster generation. If the NeoPrep run included quantification, see the suggested clustering recommendations on the support pages for your library prep kit.