Sample Sheet Creation in BaseSpace

How to Create 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 Solid 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.

Note that NovaSeq X Series has a different run set up configuration screen than other instrument platforms. Solid supports multi analysis, and in order to run Solid on NovaSeq X Series, enter the appropriate Read 1, Read 2, Index 1 and Index 2 described in the instructions below.

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 Solid supported instruments: NovaSeq 6000/6000Dx NovaSeq X Series
Secondary Analysis	Required	BaseSpace/Illumina Connected Analytics (to generate sample sheet for cloud analysis) Local
Read 1	Required on Instrument Platform NovaSeq X Series	Fill with value 151 for Solid analysis
Index 1	Required on Instrument Platform NovaSeq X Series	Fill the value depending on the Library Prep Kit used: 10
Index 2	Required on Instrument Platform NovaSeq X Series	Fill the value depending on the Library Prep Kit used: 10
Read 2	Required on Instrument Platform NovaSeq X Series	Fill with value 151 for Solid analysis
Sample Container ID	Optional	Unique Identifier for the container that holds the sample

Step 2: Configuration

Note: On NovaSeq X Series, this page is called "Configuration 1". The right hand corner of the UI displays the Read 1, Read 2, Index 1 and Index 2 entered on the previous run settings screen.

Parameter Name	Required	Description
Application*	Required	DRAGEN Solid WGS Tumor Only Pipeline
Description	Optional	Optional text field
Library Prep Kit	Required	-Illumina DNA Prep Kit. -Illumina DNA PCR Free Prep Kit
Index Adapter Kit	Required	[TODO]

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 Not applicable on NovaSeq X Series	Auto filled with the standard values, but can be optionally overwritten.
Override Cycles	Required on NovaSeq X Series	Entered based on Run Settings read lengths & index 1 / index 2
Lane Usage	Not applicable on NovaSeq X Series or NextSeq 1000 / 2000	Checkbox allows users to apply the same lane across samples.
Lane	Required if Lane Usage is unchecked Not applicable on NextSeq 1000 / 2000	Specify lanes for each sample. The unmarked checkbox at the top of the dropdown selects all lanes.
Case ID	Optional	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.
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 Solid from BCL files, set the value to False. If auto-launching Solid from FASTQ after auto-launching BCL Convert, set the value to True.
DNA Barcode Mismatches Index 1** DNA Barcode Mismatches Index 2** RNA Barcode Mismatches Index 1** RNA Barcode Mismatches Index 2**	Required on NovaSeq X	Default value is set to 1. These fields are required by NovaSeq X and represent BCL Convert settings for index diversity checks when demultiplexing. These values are not used in Solid analysis.

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.

For NovaSeqX Plus users, the run can be saved as a draft or as a planned run (via “Save as Draft” and “Save as Planned” buttons respectively). Either selection will save the run to the Planned Runs screen on BaseSpace. There is no option to export the sample sheet on this screen.

Planned Runs Screen (NovaSeq X Series only)

The Planned Runs screen lists all planned or drafted runs. Users can set drafted runs to planned, export the sample sheet, and edit or delete a run on this screen.

Once the run is saved as Planned, it will appear on the NovaSeq X Series instrument where it can be selected for sequencing.

For more information on run planning, refer to the BaseSpace Sequence Hub support site page.

Guided Examples based on TSO 500

Please review these guided examples of TSO 500 analysis workflows that include a step of setting up a run in BaseSpace Run Planning tool:

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