Questions & Answers

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  • What additional functionality does cBot 2 offer?

    The cBot 2 offers positive sample tracking for the cluster generation step of the sequencing workflow. The instrument records the barcode ID of the reagents, flow cell, library template, and any custom or additional primers used for a run. You can configure your cBot 2 to share those IDs with LIMS, or work in standalone mode.

  • Can I upgrade my cBot to a cBot 2?

    No. The cBot 2 was specifically designed to provide positive sample tracking.

  • Are original cBot manifolds compatible with cBot 2?

    No, original manifolds do not align correctly on the new instrument.


  • How can I optimize cluster formation?

    Short fragments tend to create smaller clusters, allowing greater data density. The optimal fragment size for a single-read run is 150–300 bp. The optimal fragment size for a paired-end run is 250–500 bp.

  • What is the recommended DNA concentration for cluster generation?

    The first time you process template DNA, try a concentration titration range to optimize the number of clusters formed. If the concentration is too low, fewer clusters are generated and result in a low sequencing yield. If the concentration is too high, clusters are too dense and can complicate data analysis. For more information, see the Sequencing Library qPCR Quantification Guide (part # 11322363) (a MyIllumina login is required) or the HiSeq and GAIIx Systems Denature and Dilute Libraries Guide (part # 15050107).

  • Can I cluster any Illumina library type on the cBot 2?

    Yes, but make sure that the library type you cluster on the cBot 2 is compatible with your sequencing instrument. For example, HiSeq X is compatible with TruSeq Nano DNA and TruSeq DNA PCR-Free libraries only.

Reagents and Flow Cells

  • Can I use cBot cluster kits on the cBot 2?

    Yes. All cluster kits intended for use on the cBot are also compatible with cBot 2.

  • Why do I need to use a keyed 8-tube strip for libraries?

    Using the keyed 8-tube strip is important for sample tracking. Use Seahorse Bioscience catalog # 204026-100, which provides keyed 8-tube strips with barcode labels designed specifically for use on the cBot 2.

  • Can I use strip tubes without barcode labels on the cBot 2?

    For libraries, you can use unlabeled 8-tube strips on the cBot 2 only for runs without sample tracking. Use an unlableled 8-tube strip for all custom or additional primers, regardless of run type.

  • Can I cluster a GA flow cell on the cBot 2?

    You can cluster a GA flow cell on the cBot 2, but sample tracking is available only for clustering a HiSeq flow cell (excepting TruSeq Rapid flow cells). To perform cluster generation on a GA flow cell, you must turn off sample tracking and change the adapter plate. Dedicating a cBot 2 to 1 platform avoids routinely reconfiguring the instrument for sample tracking. For instructions on changing the adapater plate, see the cBot 2 System Guide (document # 15065681).


  • How do I enable positive sample tracking?

    The positive sample tracking option is enabled by default. For more information about sample tracking and other configuration options, see the cBot System Configuration Guide (document # 1000000005301).

  • Where is barcode information stored for the sample tracking workflow?

    Barcode information is recorded and stored in the run data file (*.xml). This file is written to a preferred network location, which you can configure from the LIMS tab.

  • How do I connect to LIMS?

    In Configuration, select the LIMS tab and then select the Enable LIMS checkbox. Select the LIMS Server field and enter your LIMS server name using the onscreen keyboard. To generate a run data file (*.xml) for use with LIMS, select the Generate File with Experiment Information checkbox and specify a network location for the output. For more details, see the cBot System Configuration Guide (document # 1000000005301).

  • Which barcode scanner do I use to record consumable IDs?

    For runs with sample tracking, consumables are scanned internally after they are loaded onto the instrument and the lid is closed. Use the exteranl scanner to record consumable IDs for runs without sample tracking.

    If a consumable cannot be scanned internally, the software provides options for using the external scanner or onscreen keyboard. Sample tracking is not available for consumables that are not scanned internally, but the barcode IDs are always stored in the run data file, regardless of sample tracking.

  • Can I use an original cBot manifold on the cBot 2?

    No. The cBot 2 manifold includes clearances to allow the flow cell scanner to read the flow cell barcode. The new manifolds replace the existing manifolds in all cBot cluster kits.


  • What software is compatible with cBot 2?

    Use cBot software v3.0.40 or later. Previous versions of cBot software are not compatible.