Instrument Integration

The platform supports routing sequencing run outputs from sequencing instruments to the platform storage to be accessed through the platform GUI or the Genomic Data Store (GDS) APIs. Sequencing outputs can then be used in secondary analysis pipelines. Integration capabilities are currently limited depending on the instrument used. BaseSpace Sequence Hub (BSSH) is required in order to configure the sequencing run to output to the platform.

Instrument integration is currently limited to NextSeq 1000/2000 and NovaSeq 6000 instruments

Prerequisites

  • BaseSpace Sequence Hub (BSSH) enabled for the domain

  • Workgroup created with access to BSSH and ICA

  • Workgroup owner must enable Transfer FASTQs to ICA feature in the Settings on their workgroup in BSSH

  • Project created in the platform GUI

  • Project shared with the workgroup with the Contributor role assigned

  • User performing the sequencing run must be assigned the HasAccess role for BSSH and ICA applications in the workgroup

🚧 Important

The Transfer FASTQs to ICA setting in BSSH must be made visible for a domain by an Illumina representative

🚧 Important

The configuration below will result in duplicate copies of all FASTQ datasets - one in the workgroup context in BSSH and one in the project context in the platform. Storage costs will be incurred for both sets of files. For information on how to delete the workgroup dataset, contact your Illumina Representative.

Sample Sheet Configuration

The end-to-end workflow flow for sequencing run outputs to be routed to the platform correctly starts with correctly configuring the samplesheet used for the sequencing run.

  • v2 SampleSheet is required

  • In the [Cloud_Data] section, the ProjectName column values must exactly (case-sensitive) match the name of the project created in the platform.

  • In the [Cloud_Settings] section, the value of BsshApp (appslug) must be set to illumina-inc.bcl-convert.1.2.0

For NextSeq2000, you can generate this sample sheet by using the BSSH run planning tab and choosing BCLConvert for your Cloud Orchestrated Cloud Analysis workflow

Reference the v2 Sample Sheet template for guidance.

BSSH Configuration

BaseSpace Sequence Hub (BSSH) provides the management interface for setting up and tracking the sequencing run.

To configure BSSH to send sequencing run outputs to the platform, first login to BSSH and switch to the workgroup context for the workgroup setup with the project in the platform GUI (see Prerequisites).

Navigate to the Settings for the workgroup.

In the Account settings section, enable the "Transfer FASTQs to ICA" toggle switch. This will configure the workgroup to always use this setting for all future sequencing runs.

Instrument Setup

The v2 SampleSheet is placed into the run folder on the instrument. Login to the instrument control software using the user within the workgroup from the steps above to initiate the sequencing run.

When the sequencing run completes and the run outputs files have been uploaded to BSSH, the BCL Convert application will automatically run to covert the run output BCL files to FASTQ files. These FASTQ files and their associated Samples will then show up in the platform GUI after the transfer completes.

View Samples

On the first run upload and BCL Conversion completion, a new volume in the project context will be created (gds://samples-cid.{project Identifier}). Each sample provided to the run will result in a new directory created within this volume in the platform storage service named with a unique identifier based on the sample resource ID.

The content of the sample directory, including the associated FASTQ files, will show up in the platform GUI data section for the project, within the "runs" folder. The sample resource information will appear in platform GUI in the samples section of the project. With the samples and the associated FASTQs available from the platform GUI, Pipelines in the platform may be executed with the files provided as inputs.

The time for samples to appear in the platform GUI may vary depending on system load and number of FASTQ files included in the output.

Samples and associated FASTQ files will be tagged with information from the upstream instrument run and demultplexing step.

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