Run Workflows
Cloud Orchestrated Cloud Analysis
The Cloud Orchestrated Cloud Analysis workflow streamlines sequencing run planning and cloud-based secondary analysis using the BaseSpace Sequence Hub Run Planning interface. With Cloud Orchestrated Cloud Analysis, you can plan a sequencing run for a specific instrument platform and configure the associated cloud secondary analysis using the BaseSpace Sequence Hub Run Planning interface. Once the run has been planned, any instrument of that platform can access and kick off the run, provided you log into the instrument using the same workgroup context as the run was planned in.
Sequencing runs using this workflow require you to upload your run data to BaseSpace Sequence Hub so that it can be used to run the associated secondary analysis.
Once the sequencing run is complete and all primary analysis data has been uploaded to BaseSpace Sequence Hub, the secondary analysis is automatically kicked off in the cloud and linked to the run in BaseSpace Sequence Hub.
Cloud Orchestrated Local Analysis
The Cloud Orchestrated Local Analysis workflow enables you to plan your sequencing run (associated with a specific instrument platform) and the associated on-instrument secondary analysis using the BaseSpace Sequence Hub Run Planning interface. Once the run has been planned, any instrument of that platform can access and kick off the run, provided you log into the instrument using the same workgroup context as the run was planned in.
Sequencing runs using the Cloud Orchestrated Local Analysis workflow require you to send at least run monitoring data to BaseSpace Sequence Hub so that the run planned in the cloud can be kept in sync with the instrument.
Once the sequencing run is complete and all primary analysis data has been generated, the secondary analysis is automatically kicked off on the instrument as specified by the user during run planning.
Locally Orchestrated Local Analysis
The Locally Orchestrated Local Analysis workflow enables you to plan a sequencing run and associated on-instrument secondary analysis using the on-instrument Run Planning interface. Once the run has been planned, any user can access and kick off the run upon logging into the instrument.
Once the sequencing run is complete and all primary analysis data has been generated, the secondary analysis is automatically launched on the instrument, as specified by the user during run planning.
Sequencing runs using the Locally Orchestrated Local Analysis workflow enable you to use any level of cloud connectivity and data upload. On NovaSeq X Series or MiSeq i100 Series instruments, you can also optionally upload FastQ and BAM/CRAM files to the cloud if desired.
Manual Run with Sample Sheet Based Local Analysis
The Sample Sheet Driven Local Analysis workflow leverages DRAGEN on the instrument, relying on a sample sheet to provide the necessary details for orchestrating and executing the analysis directly onboard. In order to use this workflow, select the option when setting up a run to perform local analysis using a sample sheet, and attach the desired sample sheet to your run.
When using this workflow, the DRAGEN analysis is started onboard automatically when the sequencing data is in a ready state to begin analysis.
For optimal results, it is recommended to generate the initial sample sheet using the BaseSpace Sequence Hub Run Planning interface for local analysis. This will ensure proper formatting and acceptable values for all fields.
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