BaseSpace® Clarity LIMS integration with NovaSeq™ Series Instruments

Despite advances in sequencing technology, conducting studies from an informatics perspective can still be challenging. Managing, analyzing, and interpreting the large volume of data generated from genomic studies calls for a systematic, standardized, and pipeline-centric approach.1

To accommodate this type of approach, we have integrated BaseSpace Clarity LIMS and the NovaSeq Series instruments. The integration helps expedite genomic workflows and can potentially reduce human error inherent when handling and managing samples in a laboratory.

Ready to use, this integration connects BaseSpace Clarity LIMS to the NovaSeq instrument with automated tracking and file generation. Users of both systems can:

  • Apply a pipeline-based approach from sample accessioning to secondary analysis of the data.
  • Positively track samples from sample accessioning to secondary analysis through automation and validation of sample indexes and reagent barcodes.
  • Automate sequencing run information and parse key sequencing metrics from the instrument back into BaseSpace Clarity LIMS.
  • Initiate secondary analysis by streaming sequencing information directly to BaseSpace Sequence Hub.


The protocol provides a series of validated steps, as noted in the illustration, below.

The NovaSeq Series preconfigured protocol as seen in BaseSpace Clarity LIMS.

Additionally, the integration has several points at which users can validate the integration and efficiently test it before putting into production. These points include:

Integration validation point 1

BaseSpace Clarity LIMS automatically calculates library normalization and pooling volumes. BaseSpace Clarity LIMS generates the run info file and the NovaSeq Sample Sheet including the Library tube ID, which are automatically placed into a specific network folder on the instrument.

Integration validation point 2

Key primary sequencing metrics, such as Yield, %Q30, %Reads PF, Number of reads, etc., are automatically parsed into BaseSpace Clarity LIMS. This parsing enables users to generate sequencing statistics and monitor sequencing instrument performance over time.

Integration validation point 3

NovaSeq 6000 integrates with BaseSpace Sequence Hub, where sequencing run details and sequencing data are automatically sent, thus making the triggering of downstream analysis even easier.

The complete integration is available for BaseSpace Clarity LIMS Gold users, although a more simplified version is available to all BaseSpace Clarity LIMS users. Additionally, the integration is currently compatible with S2 flowcells; additional functionality will become available to the integration when new flowcells are available.

For more information about this integration, please contact us.

For Research Use Only. Not for use in diagnostic procedures.
  1. “Big Biological Data: Challenges And Opportunities”. N.p., 2017. Web. 17 Apr. 2017.

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