Run Planning with the BSSH Run Planner Tool

To plan a successful sequencing run, a sample sheet with details on run configuration (e.g., sequencer type, flowcell, and sample type) is required. Follow the instrument-specific steps below to create a sample sheet compatible with the Illumina Prep Kit and DRAGEN Protein Quantification.

BSSH Run Planner with NovaSeq 6000

1. Log in to BaseSpace Sequence Hub and select your workgroup.

2. In the Run Planning tool, configure the settings described in the following table. Some settings are instrument specific. When you select the DRAGEN Protein Quantification application, the library prep kit and index adapter kit populate automatically, along with additional instrument-specific settings.

This table describes the possible configuration settings and values.

Setting	NovaSeq 6000 Value
Instrument Platform	NovaSeq 6000/6000Dx
Secondary Analysis	[Cloud analysis] BaseSpace/Illumina Connected Analytics [Local analysis] Local
Application	DRAGEN Protein Quantification (select the latest version)
Library Prep Kit	Illumina Protein Prep 9k (auto-populated)
Index Adapter Kit	Illumina DNA-RNA UD Indexes Set A B C D Tagmentation (auto-populated)
[NovaSeq 6000]	These settings are configured automatically and are not editable. - 2 indexes - Single Read - 15, 10, 10, 0

1. Lane Splitting is not supported for NovaSeq 6000 runs. Select "Repeat set of samples across all lanes."

2. Upload Illumina Protein Prep Automation System output file (*.csv) to BSSH Run Planner.

   • Select Import samples, select the CSV file type, and upload the Illumina Protein Prep Automation System output file. The interface highlights invalid values immediately after the file is rendered.

   • [Optional] To include a second plate in the run, repeat the import process and select Add to existing samples when prompted. The new samples are appended to the samples that were uploaded previously.

   WARNING - Sample IDs and index sequences must be unique within a sequencing run. If combining libraries from multiple Illumina Protein Prep runs, avoid combining plates that contain the same sample IDs or index sequences.

3. [Optional] Multi-project analysis: Users may add Project values either in the Illumina Protein Prep output file (prior to uploading) or add values in the BSSH Run Planner. See Lane Splitting and Multi-Analysis by Project for more details. WARNING - All samples from the same plate must have the same project (or no project) value.

4. [Optional] Enter an appropriate output file prefix. This value is used as a part of the prefix for the secondary analysis output file names. The first character must be alphanumeric. For the remaining characters, alphanumeric, hyphens, underscores, and spaces are permitted.

5. Proceed to the Run Review page and save the planned run.

   • [NovaSeq 6000, cloud analysis] Download the sample sheet and save it to a network location accessible to the sequencing instrument.

   • [NovaSeq 6000 Local analysis] Select Export to download the sample sheet. Save the file to a network location accessible to the sequencing instrument.

For additional information on run planning, refer to the BSSH Plan Runs documentation.

BSSH Run Planner with NovaSeq X

1. Log in to BaseSpace Sequence Hub and select your workgroup.
2. In the Run Planning tool, configure the settings described in the following table. Some settings are instrument specific. When you select the DRAGEN Protein Quantification application, the library prep kit and index adapter kit populate automatically, along with additional instrument-specific settings.

This table describes the possible configuration settings and values.

Setting	NovaSeq X Value
Instrument Platform	NovaSeq X Series
Secondary Analysis	[Cloud analysis] BaseSpace/Illumina Connected Analytics [Local analysis] Local
[Local analysis] FASTQ file compression format	DRAGEN This setting is required by default. The setting does not impact DRAGEN Protein Quantification as no FASTQ files are output.
[Local analysis] Generate FastQC metrics	Yes This setting is optional. The setting does not impact DRAGEN Protein Quantification as no FASTQ files are output.
Read Lengths	- Read 1: 15 - Index 1: 10 - Index 2: 10 - Read 2: 0
Application	DRAGEN Protein Quantification (select the latest version)
Library Prep Kit	Illumina Protein Prep 9k (auto-populated)
Index Adapter Kit	Illumina DNA-RNA UD Indexes Set A B C D Tagmentation (auto-populated)
Override Cycles	These settings are configured automatically and should not be edited. - Read 1: Y15 - Index 1: I10 - Index 2: I10

1. If lane splitting will be utilized with this sequencing run, it's recommended to add values to Lane column to Illumina Protein Prep Automation System output files locally. See Lane Splitting and Multi-Analysis by Project for more details.

   1. If lane splitting is not utilized, do not edit the Lane column in the Illumina Protein Prep Automation System output file.

2. Upload Illumina Protein Prep Automation System output file (*.csv) to BSSH Run Planner.

   • Select Import samples, select the CSV file type, and upload the Illumina Protein Prep Automation System output file. The interface highlights invalid values immediately after the file is rendered.

   • [Optional] To include a second plate in the run, repeat the import process and select "Add to existing samples" when prompted. The new samples are appended to the samples that were uploaded previously.

   • Barcode mismatch 1 and 2—No action is required. The default value is set to 1. Do not change this value.

   • If lane splitting will not be utilized, indicate that each sample is present in all lanes. For the first sample, click on the Lanes box and select the first checkbox. This will populate the cell with "1,2,3,4,5,6,7,8". Then, select the Lanes header and click "Fill down". This will add these lane values for all samples.

   

   

   WARNING - Sample IDs and index sequences must be unique within a sequencing run. If combining libraries from multiple Illumina Protein Prep runs, avoid combining plates that contain the same sample IDs or index sequences. When combining libraries with non-unique indexes, ensure they are loaded into different flow cell lanes, and that lane splitting is enabled during sample sheet creation.

3. [Optional] Multi-project analysis: Users may add Project values either in the Illumina Protein Prep output file (prior to uploading) or add values in the BaseSpace Run Planner. See Lane Splitting and Multi-Analysis by Project for more details. WARNING - All samples from the same plate must have the same project (or no project) value.
4. [Optional] Enter an appropriate output file prefix. This value is used as a part of the prefix for the secondary analysis output file names. The first character must be alphanumeric. For the remaining characters, alphanumeric, hyphens, underscores, and spaces are permitted.

5. Proceed to the Run Review page and save the planned run.

   • [NovaSeq X Series, cloud analysis] No action is required. The sample sheet is automatically uploaded to the instrument.

   • [Local analysis] Select Export to download the sample sheet. Save the file to a network location accessible to the sequencing instrument.

For additional information on run planning, refer to the BSSH Plan Runs documentation.

Additional Notes:

• DRAGEN Protein Quantification does not support Multiple Analysis on NovaSeq X.