NovaSeq X Run Planning - DRAGEN Germline

This page gives an overview of how to plan a run on BaseSpace for the NovaSeq X Series using Cloud DRAGEN Germline analysis for the Illumina TruPath Genome workflow.

BaseSpace Sequence Hub (BSSH) Run Planning is used to generate a valid sample sheet in v2 format compatible for use on NovaSeq X Sequencing Systems. Filling out the run planning input form will produce a sample sheet with the required fields filled in that can be used to auto-launch the DRAGEN Germline Analysis for use with the Illumina TruPath Genome workflow. Refer to Cloud Analysis Auto-launch for more information about the Run Planning/ Autolaunch.

For information on the supported variant callers in the Run Analysis settings, refer to the Cloud Analysis Settings section.

To navigate to Run Planning, open BaseSpace Sequence Hub and navigate to the Runs page by using the navigation bar or by opening the menu on the left-hand side. From the New Run dropdown menu select Run Planning.

1. Access the appropriate workgroup to plan the sequencing run

2. Select "Runs" from the top panel

3. Select "New Run"

4. Select "Run Planning" from the right-hand dropdown

Step 1: Specify Run Settings

The run settings specifications are described below.

Descriptions

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 8192 characters except square brackets, asterisks, and commas.
Instrument Platform	Required	Select "NovaSeq X Series" from the dropdown.
Secondary Analysis	Required	Select "BaseSpace / Illumina Connected Analytics" from the dropdown.
Read 1	Required	151 for DRAGEN Germline analysis.
Index 1	Required	Set to "0" Indexing is not supported.
Index 2	Required	Set to "0" Indexing is not supported.
Read 2	Required	151 for DRAGEN Germline Analysis.
Sample Container ID	Optional	Unique identifier for the container that holds the sample.

Step 2: Specify Configurations

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

The run configuration settings specify the analysis options for the run, as shown below.

Descriptions

Parameter Name	Required?	Description
Application	Required	Select "DRAGEN Germline - 4.5.2" for compatibility with Illumina TruPath Genome. Note that a message will appear to use the Illumina TruPath Genome kit and flow cell with this application version.
Description	Optional	Optional Text Field
Library Prep Kit	Required	Select "Illumina TruPath Genome Prep (C2, 2 Samples" or "Illumina TruPath Genome Prep (C8, 8 Samples)" from the dropdown.
Index Adapter Kit	Required	Select "Not Applicable" as indexing is not supported.
Reference Genome	Required	Select "Homo sapiens [1000 Genomes] hg38 v6" from the dropdown. Note that TruPath is only compatible with Hg38 reference.
Read 1	Required	151 for DRAGEN Germline Analysis.
Index 1	Required	Set to "0" Indexing is not supported.
Index 2	Required	Set to "0" Indexing is not supported.
Read 2	Required	151 for DRAGEN Germline Analysis.
Sample Container ID	Optional	Unique identifier for the container that holds the sample.

Step 3: Specify Run Configuration and Analysis Settings

The run configuration settings specify the analysis settings required for enabling proximity mode in DRAGEN Germline for use with the Illumina TruPath Genome workflow.

Descriptions

Parameter Name	Required?	Description
Description	Optional	Optional Text Field
Library Prep Kit	Required	Auto-populated from previous step
Index Adapter Kit	Required	Auto-populated from previous step
Reference Genome	Required	Auto-populated from previous step
Variant Callers	Required	Select "None" for running Mapping/Align only. Select "Small" for a subset of Variant Callers. Select "All" for running all Variant Callers. For more information on the supported callers for Autolaunch, refer to this section.
QC Coverage Regions 1	Optional	File in BED format used to generate a QC coverage region report
QC Coverage Regions 2	Optional	File in BED format used to generate a QC coverage region report
QC Coverage Regions 3	Optional	File in BED format used to generate a QC coverage region report
QC Cross Contamination Variants	Optional	QC file in VCF file format
Adapter Read 1	Required	Pre-populated with default setting
Adapter Read 2	Required	Pre-populated with default setting
Sample Table	Required	Lanes and Sample ID should be filled out based on how the sample will be prepared. Please refer to the Illumina TruPath Genome Assay Guide for additional information. The optional Project field is used to specify the associated BaseSpace Project to output data to. If left empty, Project will default to the Project name derived from the Experiment/Run name. Note: Only one sample per lane is allowed. Up to two samples may be specified using the C2 flow cell, while up to eight samples may be specified using the C8 flow cell. Note: Sample IDs must be unique for each Sample. If the sample is repeated in another run, select a new name. BSSH will combine sequencing data from samples with the same sample ID.
Map / Align Output Format	Required	Select "BAM"
Enable Proximity Analysis	Required	Select "Yes" New analysis setting which enables the proximity analysis workflow in DRAGEN Germline. Required for use with Illumina TruPath Genome workflow.
Enable Proximity Visualization	Optional	Optional setting used for outputting *.hic files for visualization. Additional run time and compute may be incurred. Refer to Visualizations section here: Visualize in HiGlass

Step 4: Specify Run Configuration and Analysis Settings

Once all details are captured and pass validation, review the run information and choose the Edit option to correct any information.

For NovaSeq X Sequencing Systems, the run can be saved as a draft or as a planned run (via Save as Draft and Save as Planned buttons respectively). Once a run is saved as Planned, it will appear on the NovaSeq X Series instrument where it can be selected for sequencing.

For more information about the auto-launch, refer to Cloud Analysis Auto-launch. For additional information on run planning, refer to Plan Runs on Basespace Sequence Hub.