Run Planning

How to Create DRAGEN StrataMap Runs in the BaseSpace Run Planning Tool

The BaseSpace Sequence Hub (BSSH) Run Planning tool is used to generate a planned run or an exportable sample sheet in v2 format for use on the NovaSeq 6000 and NovaSeq X Series systems, which can kick off an Autolaunch analysis.

The Run Planning tool can also be used to generate a sample sheet for use with Core Manual Launch. If Autolaunch is not desired for secondary analysis, please see the Core Manual Launch subsection before continuing.

Optional: For more information on fields that appear in Core sample sheets, refer to the Sample Sheet section of this guide.

Prior to setting up DRAGEN StrataMap runs in BSSH Run Planning, ensure that image processing is complete after the Illumina StrataMap Image Tool and that sample images have been successfully exported to the selected Core location and BaseSpace Workgroup.

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

Step 1: Run Settings

Log into BSSH using your Illumina account credentials and select your desired workgroup from the account dropdown menu in the upper right corner of the home screen.

From the home screen, select Runs.

Select the New Run dropdown menu and select Run Planning.

Enter parameters and select Next to move forward.

For more details on Run Settings parameters, refer to Table 1.

Note: The NovaSeq X Series run setup configuration is different compared to other instrument platforms and allows for multiple analysis configurations for a planned run. DRAGEN StrataMap is not compatible with other analysis configurations without manual adjustments see instructions here.

Table 1. Run Setting Parameters

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 character, a dash, or an underscore.
Run Description	Optional	Run Description can contain 255 characters except square brackets, asterisks, or commas.
Instrument Platform	Required	Choose from the following supported instruments: NovaSeq 6000/6000Dx NovaSeq X Series
Secondary Analysis	Required	Select BaseSpace/Illumina Connected Analytics (to generate a sample sheet for cloud analysis). Local is not supported at this time.
Read 1	Required on Instrument Platform NovaSeq X Series	Fill with value 130 for DRAGEN StrataMap analysis.
Index 1	Required on Instrument Platform NovaSeq X Series	Fill with value 8 for DRAGEN StrataMap analysis.
Index 2	Required on Instrument Platform NovaSeq X Series	Fill with value 0 for DRAGEN StrataMap analysis.
Read 2	Required on Instrument Platform NovaSeq X Series	Fill with value 0 for DRAGEN StrataMap analysis.
Sample Container ID	Optional	Unique identifier for the container that holds the sample.

Step 2: Configuration

Note: On the 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 values entered on the previous Run Settings screen.

Select DRAGEN StrataMap - 2.1.0 from the dropdown menu in the Application section. The library prep kit and index adapter kit will auto-populate based on the application selection.

To move forward, select Next.

For more information on Configuration Parameters, see Table 2.

Table 2. Configuration Parameters

Parameter Name	Required	Description
Application	Required	DRAGEN StrataMap v2.1.0
Description	Optional	Optional text field
Library Prep Kit	Required	Automatically set to Illumina StrataMap Prep
Index Adapter Kit	Required	Automatically set to Illumina StrataMap Prep

Step 3: Import Samples from Illumina StrataMap Image Tool

There are two options for importing sample information into the sample sheet for DRAGEN StrataMap analysis. You may select "From BSSH files" or "From this computer" if the output from the Illumina StrataMap Image Tool was exported locally and to cloud at the same time.

If the output from the Illumina StrataMap Image Tool was exported to one location only (local or BSSH), use the corresponding method below to select sample information.

Selecting "From BSSH Samples":

1. Select the "Import Samples" button at the top of the samples table.
2. Select "From BSSH files".
3. Within the file selection box, browse or search for the samples file using the Slide ID of the experiment and press Select.
4. Once imported, the samples will appear in the samples table as well as in the per-sample configuration table at the bottom of the page. Review the samples and image file names to ensure they are correct.

Selecting "From this computer":

1. Select the "Import Samples" button at the top of the samples table.
2. Select "From this computer".
3. Navigate to the location where the "samples_for_slide.csv" file was stored upon local export from the Illumina StrataMap Image Tool.
4. Once imported, the samples will appear in the samples table as well as in the per-sample configuration table at the bottom of the page. Review the samples and image file names to ensure they are correct.

There will be an expected error after you select and fill in the table with either of the above options. This message can be ignored with no further intervention. To move forward, simply close the message.

Screenshot of the expected error message

Step 4: Complete Sample & Analysis Settings

Once samples from the Illumina StrataMap Image Tool have been imported, fill out the remaining fields. For additional details, refer to Table 3.

Table 3. Sample and Analysis Parameters

Parameter Name	Required	Description
Read Lengths: Read 1 and Read 2	Required for NovaSeq 6000. Not applicable on NovaSeq X Series.	Auto-filled with the standard values, but can be optionally overwritten.
Lane Usage	You may select the checkbox to "Repeat set of samples across all lanes" or select all lanes manually via the dropdown menu within each row of the table	The checkbox allows users to "Repeat set of samples across all lanes".
Lanes	Required	Specifies lanes for each sample. Select the unmarked checkbox at the top of the dropdown to select all lanes.
Project	Optional	Optional field to describe the associated project.

Analysis Settings:

Enter Analysis Settings parameters. For more information on parameters, see Table 4.

Upon completion of configuring parameters, select Next to move forward to Run Review.

Table 4. Analysis Settings Parameters

Setting Name	Required	Description
Reference Genome	Required	Selected from the following supported genomes: Homo sapiens [1000 Genomes] hg38 v* Mus Musculus [UCSC] mm39* Note: If you shared a custom genome of interest with an Illumina representative, it will be shown here.
Grid Bin Size	Required	Define the size of grid bins in μm. The recommendation is to use 10μm; the minimum bin size is 5μm. Multiple sizes can be specified using an array of integers delimited by colons, e.g., 5:10:25 for bin sizes 5, 10, and 25 μm. Use of multiple bin sizes will increase computation time and cost.
Cell Boundary Expansion Distance	Required	Used in cell segmentation. Sets the cell expansion distance from the cell nucleus, in μm. The recommendation is 5μm.
Map Align Output Format	Required	The recommendation is to keep this set to "None". Generating BAM files will require additional compute and storage costs.

Step 5: Run Review

Once all details have been entered and pass the system check, the details can be reviewed on the Run Review screen. On this page, details from previous steps can be edited, or the sample sheet can be exported. Select Export to export the sample sheet.

For NovaSeq 6000: After exporting the sample sheet, click "Cancel" to finish run planning.

Note: After leaving by selecting "Cancel", the run and sample sheet will not be accessible.

For NovaSeq X Series: The run can be saved as a draft or as a planned run (via "Save as Draft" or "Save as Planned", respectively). Either selection will save the run to the Planned Runs screen within BSSH.

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.