Sequencer Run Upload

Sequencer run output data produced by Illumina sequencing instruments is uploaded to ICA storage.

BaseSpace Setup

BaseSpace Sequence Hub (BaseSpace) is used to plan and monitor sequencing runs. BaseSpace settings must be configured to send sequencing run data to ICA prior to sequencing. For workgroups, this must be confiugred by the workgroup administrator. Workgroup users have read-access to the toggle switch setting, but cannot modify it.
Navigate to the BaseSpace Settings view. In the "Settings" section, set the "ICA Run Storage" setting to ON.
This setting is not necessary for NovaSeq X Series instrument type
The visibility of the "ICA Run Storage" configuration setting is controlled by Illumina support. Contact Illumina Support to request the setting be made available for your domain.
ICA Run Storage toggle

Sequencer Run Data

Sequencer run data uploaded directly to ICA via CLI or Service Connector to a user-manaaged project will not be available in BaseSpace.
Sequencer run data is stored in ICA 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 ICA 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 "[email protected]".
BaseSpace externally managed project
The project contains the following tags:
  • Technical Tags: bssh.project.user:{user/workgroup ID}
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 ICA.

Upload Sequencing Run Data

Sequencer run data stored outside of ICA or BaseSpace may be uploaded using the BaseSpace CLI (command-line interface) to make it available in both BaseSpace and ICA.
Use the BaseSpace Uploading a run instructions to upload a sequencer run output folder.
The "ilmn-runs" folder contains all sequencer run data managed by BaseSpace and should not be linked to a user-managed project. Only link individual sequencer run output folders within the ilmn-runs folder.
Sequencer Run Data and analysis output data stored in the BaseSpace externally-managed project can be linked to a user-managed project for use in downstream analyses in ICA.