Cloud Analysis Auto-launch

Sequencer Run Data in Illumina BioInsight Platform Core

Sequencer run data is stored in Illumina BioInsight Platform Core in an externally-managed project created by BaseSpace. Operations in BaseSpace, including planning and monitoring instrument runs, are performed in a given user or workgroup context. To preserve permission boundaries between applications, an externally-managed project is created for each user/workgroup context per region. The Illumina BioInsight Platform Core project will be named using the convention BSSH {context name}, where {context-name} is the user or workgroup name operating in BaseSpace. For workgroups, the project will be created on behalf of the workgroup owner. The project Team includes an entry for the workgroup to grant all workgroup users read-only access to the project. While Team members may be assigned the Contributor role in the externally-managed project, they will not have write access (ie, create/delete data, run pipelines) in the project.

In the example below, the project is created for a workgroup with name "Research" where the workgroup owner is "bsadmin@illumina.com".

The project contains the following tags:

For workgroups, users who are members of the workgroup will have access to the data in the externally-managed project.

All sequencing run data is stored in the ilmn-runs folder. Within that folder, the data for each sequencing run is stored in a sub-folder named based on the run name used to create the run during run planning (or as specified in the RunName row of the [Header] section in the sample sheet) appended with a unique identifier.

The screenshot below provides an example of a sequencer run output folder uploaded to Illumina BioInsight Platform Core.

Automated Secondary Analysis in Illumina BioInsight Platform Core

When the sequencing run data upload has completed, the post-sequencing secondary analysis described in the sample sheet will be automatically started.

In Illumina BioInsight Platform Core, secondary analyses launched after a sequencing run completes is orchestrated by a parent process called a Workflow Session. The workflow session serves as a parent process orchestrating the secondary analysis, including launching secondary analysis pipelines and creating sample entities in Illumina BioInsight Platform Core.

Upon completion of the sequencing run data upload, a workflow session record is created and visible in the Illumina BioInsight Platform Core "Analyses" view. The workflow session record can be identified by the User Reference, which will have "ws" preceding the run name.

The workflow session details view includes a section Orchestrated Analyses to indicate analyses launched by the workflow session as part of the automated secondary analysis. These orchestrated analyses are driven by the information in the sample sheet, including the pipeline to launch, reference data, and sample-specific settings.

Sequencer Run Data in BaseSpace

For users intending to use BaseSpace for FASTQ generation and DRAGEN Secondary Analysis, the data will be associated with several BaseSpace Projects.

1. SampleSheet ProjectName

When using ProjectName values in Run Planning, the FASTQ files will be written to those locations.

In the SampleSheet.csv, this will be reflected in the [Cloud_Data] section.

Once BCL Convert (and any associated downstream analysis) is completed, the FASTQ files will be associated with the ProjectName specified on BaseSpace. The project column is not required to be specified, and if left blank, the FASTQ Files will be written to a BaseSpace project following the nomenclature:

2. bssh_[region]_[run ID]

For example:

bssh_use1-prod_277283070

More information about regions can be found in the BaseSpace Help center article Global Regions. The run ID corresponds to the numerical value observed in the web address bar when viewing the run.

If any DRAGEN Secondary analysis is performed, this project will also contain the DRAGEN output.