Sample Sheet Creation in BaseSpace Run Planning tool

How to Create TSO 500 Sample Sheets in BaseSpace Run Planning tool

The BaseSpace Sequence Hub Run Planning tool is available and is used to generate a valid sample sheet in v2 format for use on a TSO 500 supported sequencer for both ICA and Standalone DRAGEN Server analysis options. Filling out the form on the user interface will produce a exportable sample sheet with the required fields filled in. Refer to ICA Auto-launch Sample Sheet Requirements for descriptions of fields that appear in ICA sample sheets.

The sections below represent each step in the BaseSpace Run Planning tool.

Step 1: Run Settings

Parameter Name	Required	Description
Run Name	Required	Run Name can contain 255 alphanumeric characters, dashes, underscores, periods, and spaces; and must start with an alphanumeric, a dash or an underscore.
Run Description	Optional	Run Description can contain 255 characters except square brackets, asterisks, and commas.
Instrument Platform	Required	Choose from TSO 500 supported instruments: NextSeq 500/550 NovaSeq 6000/6000Dx
Secondary Analysis	Required	BaseSpace/Illumina Connected Analytics (to generate sample sheet for cloud analysis) Local
Sample Container ID	Optional	Unique Identifier for the container that holds the sample

Step 2: Configuration

Parameter Name	Required	Description
Application	Required	DRAGEN TruSight Oncology 500 Analysis Software - 2.5.x (with HRD) DRAGEN TruSight Oncology 500 Analysis Software - 2.5.x
Description	Optional	Optional text field
Library Prep Kit	Required	TruSight Oncology 500 TruSight Oncology 500 High Throughput
Index Adapter Kit	Required	TSO 500: TruSight Oncology 500 (NovaSeq 6000Dx, NovaSeq X, NextSeq 1000/2000) TruSight Oncology 500 (NovaSeq 6000, NextSeq 550) TSO 500 HT: TruSight Oncology 500 (NovaSeq 6000Dx, NovaSeq X, NextSeq1000/2000) TruSight Oncology 500 (NovaSeq 6000, NextSeq 550)

Step 3: Sample Settings

Users can manually enter sample information, or download a template file to bulk upload sample information. Users can import the completed template or a compatible sample sheet.

Parameter Name	Required	Description
Read Lengths: Read 1 and Read 2	Required	Auto filled with the standard values, but can be optionally overwritten.
Lane Usage	Optional	Checkbox allows users to apply the same lane across samples.
Lane	Required if Lane Usage is unchecked	Specify lanes for each sample. The unmarked checkbox at the top of the dropdown selects all lanes.
Pair ID	Required	The identifier used to pair DNA and RNA samples in a run. The field is mandatory whether a sample is part of a pair, or not. To note: The Sample ID field in the generated samplesheet will be auto-filled based on the Pair ID values captured. “_dna” and “_rna” (for DNA and RNA samples respectively) will be appended to the Pair ID value to create the Sample ID.
DNA Index ID	Required	Index set ID options are based on selected Index Adapter Kit
DNA Sample Feature	Required for TSO 500 HRD	Column appears when TSO 500 HRD application is selected. Enter for HRD enriched DNA Samples
RNA Index ID	Required	Index set ID options are based on selected Index Adapter Kit
Project	Optional	Optional field to describe the associated project
Starts from Fastq	Required	True or False If auto-launching TSO 500 from BCL files, set the value to False.

Step 4: Run Review

Once all details are captured and pass validation, the user can review the details on the Run Review screen. From here they can choose to edit details in previous screens or export the sample sheet. Once completed, press the Cancel button to finish run planning.

Note: once leaving this screen, the run and sample sheet will not be accessible.

Guided Examples

Please review these guided examples of analysis workflows that include a step of setting up a run in BaseSpace Run Planning tool:

• NovaSeq 6000Dx: TSO 500 Auto-launch Analysis in Cloud
• NextSeq 500/550Dx: TSO 500 and Connected Insights Auto-launch Analysis in Cloud