Sample Sheet

A sample sheet is required for each analysis with the DRAGEN StrataMap analysis software. A sample sheet is a comma-separated value (*.csv) file format used by Illumina instruments, platforms, and analysis pipelines to store settings and data for sequencing and analysis. The DRAGEN StrataMap analysis software is compatible with sample sheet v2. For general information on sample sheet v2, refer to Illumina Connected Software - Sample Sheet.

The analysis fails if the sample sheet requirements are not met. We recommend using the BSSH Run Planning tool to generate the sample sheet (see Run Planning).

Sample Sheet Format

The following sample sheet requirements describe required and optional fields for DRAGEN StrataMap analysis.

Use the following steps to generate a valid sample sheet:

1. Use the BaseSpace Sequencing Hub Run Planning tool to generate an example sample sheet (Run Planning) or download the sample sheet v2 template for DRAGEN StrataMap analysis.
2. If using a template, within the Sequencing Settings section, enter the following required parameters:

[Sequencing_Settings] Section

Sample Parameter	Required	Details
LibraryPrepKits	Required	Accepted value: IlluminaSpatialLibraryPrep

3. In the BCL Convert Settings section, enter the following required parameters:

[BCLConvert_Settings] Section

Sample Parameter	Required	Details
SoftwareVersion	Required	Accepted value: 4.4.0

1. In the BCL Convert Data section, enter the following parameters for each sample.

[BCLConvert_Data] Section

Sample Parameter	Required	Details
Lane	Only for NovaSeq 6000 XP, NovaSeq 6000Dx, or NovaSeq X workflows	Indicates which lane corresponds to a given sample. Enter a single numeric value per row. Cannot be empty; the analysis fails if the Lane column is present without a value in each row.
Sample_ID	Required	Must match a Sample_ID listed in the StrataMap Data section.
Index	Required	Set to "na" for each sample.

1. In the Cloud StrataMap Settings section, enter the following parameters:

[Cloud_StrataMap_Settings] Section

Setting Parameter	Required	Details
SoftwareVersion	Required	The DRAGEN StrataMap software version.
StageAllSettings	Required	Set to TRUE for DRAGEN StrataMap.
GridBinSize	Required	Array of integers delimited by colons, e.g., 5:10:25 for bin sizes 5, 10, and 25.
CellBoundaryExpansionDistance	Required	Set the cell expansion distance from the cell nucleus, in μm.
MapAlignOutFormat	Required	Recommendation is to set this to "None". Set to "bam" to generate BAM files for each sample. BAM file generation will incur additional storage and compute costs.
Genome	Required	Provide the URN to the reference genome.

1. In the Cloud StrataMap Data section, enter the following parameters:

[Cloud_StrataMap_Data] Section

Sample Parameter	Required	Details
Sample_ID	Required	Must match the Sample_ID listed in the BCL Convert Section.
ImageFile	Required	The file name of the registered image file generated by ISIT.
ImageLocation	Required	The URN of the registered image file generated by ISIT in Core.
Slide ID	Required	ID of the slide used for the spatial experiment. Only one slide is supported.

1. In the Cloud Settings section, enter the following parameters:

[Cloud_Settings] Section

Setting Parameter	Required	Details
GeneratedVersion	Not Required	The cloud GSS version used to create the sample sheet. Optional if manually updating a sample sheet.
CloudWorkflow	Not Required	ica_workflow_1
Cloud_Spatial_Pipeline	Required	This value is a universal record number (URN).

1. In the Cloud Data section, enter the following parameters:

[Cloud_Data] Section

Parameter	Required	Details
Sample_ID	Not Required	The same sample ID used in the Cloud_Spatial_Data section.
ProjectName	Not Required	The BaseSpace project name.
LibraryName	Not Required	For spatial, this is the same as the sample ID.
LibraryPrepKitName	Required	IlluminaSpatialLibraryPrep
IndexAdapterKitName	Not Required	IlluminaSpatial