DRAGEN TSO 500 Analysis Software has optional and required fields that are required in addition to general sample sheet requirements. Follow the steps below to create a valid sample sheet.
The following sample sheet requirements describe required and optional fields for DRAGEN TSO 500 Analysis Software. Depending on the deployment (standalone DRAGEN server, ICA with auto-launch, ICA with manual launch, NovaSeq 6000Dx analysis application), certain sections and required values can deviate from the standard requirements. These deviations are noted in the information below.
The analysis fails if the sample sheet requirements are not met.
Use the following steps to create a valid sample sheet.
Download the that matches the instrument & assay run.
In the Sequencing Settings section, enter the following required parameters:
In the BCL Convert Settings section, enter the following required parameters:
In the BCL Convert Data section, enter the following parameters for each sample:
Mismatches between the samples and index primers can cause incorrect results due to loss of positive sample identification. Enter sample IDs and assign indexes in the sample sheet before beginning library preparation. Record sample IDs, indexes, and plate well orientation for reference during library preparation.
In the TSO 500 Data section, enter the following parameters:
TSO 500 Data Section header changes depending on the deployment:
Standalone DRAGEN Server and ICA with Manual Launch: TSO500S_Data
ICA with Auto-launch:
To ensure a successful analysis, follow these guidelines:
Avoid any blank lines at the end of the sample sheet; these can cause the analysis to fail.
When running local analysis, using the command line, save the sample sheet in the sequencing run folder with the default name SampleSheet.csv, or choose a different name and specify the path in the command-line options.
Refer to the following requirements to create sample sheets for running the analysis on ICA with Auto-launch. For sample sheet requirements common between deployments see . Samples sheets can be created using BaseSpace Run Planning Tool or manually by downloading and editing a sample sheet template.
To auto-launch analysis from the sequencer run folder, ensure the StartsFromFastq and SampleSheetRequested fields are set to FALSE. To auto-launch analysis from FASTQs after BCL Convert auto-launch, StartsFromFastq and SampleSheet Requested fields must be set to TRUE
Refer to for this section's requirements.
This section describes fields specific for sample sheets for NovaSeq 6000Dx Analysis Application. For more information on DRAGEN TSO 500 Analysis Software sample sheet requirements, refer to the sections above.
Refer to [ for this section's requirements.
MinimumTrimmedReadLength
Required
Enter 35. Reads with a length trimmed below this point are masked.
MaskShortReads
Required
Enter 35. Reads with a length trimmed below this point are masked.
Cloud_TSO500S_DataIllumina DRAGEN TruSight Oncology 500 (HRD) Analysis Application on NovaSeq 6000Dx: TSO500HRD_Data
Sample_Description
Not Required
Sample description must meet the following requirements: - 1–50 characters. - Alphanumeric characters with underscores, dashes and spaces. If you enter a underscore, dash, or space, enter an alphanumeric character before and after. eg, Solid-FFPE_213.
IndexAdapterKitName
Not Required
The Index Adapter Kit used.
LibraryPrepKits
Required
Accepted values are:
TSO500 (for UP or CP indexes)
TSO500HT (for UDP indexes)
TSO500_v2 (for UDP v3 indexes) Analysis results may be compromised if this value does not match the index set used.
SoftwareVersion
Required
The DRAGEN component software version. For example,
TruSight Oncology 500 2.6.0 requires 3.10.17. To ensure you are using the latest compatible version, refer to the software release notes.
AdapterRead1
Required
If using TSO 500 Library Prep Kit (with UP or CP indexes): AGATCGGAAGAGCACACGTCTGAACTCCAGTCA If using TSO 500 HT Library Prep Kit (with UDP indexes): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
If using TSO500 v2 Library Prep Kit (with UCP v3 indexes):
CTGTCTCTTATACACATCT
AdapterRead2
Required
If using TSO 500 Library Prep Kit: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT If using TSO 500 HT Library Prep Kit: CTGTCTCTTATACACATCTGACGCTGCCGACGA
If using TSO500 v2 Library Prep Kit:
CTGTCTCTTATACACATCT
AdapterBehavior
Required
Sample_ID
Required
The unique ID to identify a sample. The sample ID is included in the output file names. Sample IDs must have the following characteristics:
Case-insensitive unique values
1 to 40 characters
Alphanumeric, dash, and underscore characters only
An underscore or dash must have an alphanumeric character immediately before and after
Cannot be called all, default, none, unknown, undetermined, stats, or reports.
Each sample must have a unique combination of Lane (if applicable), sample ID, and index ID or the analysis will fail.
Index
Required
Index 1 sequence valid for Index_ID assigned to matching Sample_ID in the TSO 500 Data section.
Index2
Required
Index 2 sequence valid for Index_ID assigned to matching Sample_ID in the TSO 500 Data section.
Lane
Not Required. Only for NovaSeq 6000 XP, NovaSeq 6000Dx, or NovaSeq X workflows
Sample_ID
Required
The unique ID to identify a sample. The sample ID is included in the output file names. Sample IDs are not case sensitive. Sample IDs must have the following characteristics:
- Unique for the run.
- 1–40 characters.
- No spaces.
- Alphanumeric characters with underscores and dashes. If you use an underscore or dash, enter an alphanumeric character before and after the underscore or dash. eg, Sample1-T5B1_022515.
- Cannot be called all, default, none, unknown, undetermined, stats, or reports.
- Must match a Sample_ID listed in the BCLConvert data section.
- Illumina recommends that the sample ID be based on the pair ID. Example: <Pair_ID>-DNA,<Pair_ID>-RNA.
Sample_Type
Required
Enter DNA or RNA.
For HRD samples, this parameter must be DNA.
Pair_ID
Required
A unique ID that links DNA and RNA from the same biological sample from the same individual. Pair ID shares, at most, one DNA and one RNA sample per run. eg, if a Sample_ID is TestSample1-DNA for DNA and TestSample1-RNA for RNA, the Pair_ID TestSample1 will link these samples that are on different rows in the sample sheet together.
If the pair ID is associated with more than one DNA or RNA sample, the analysis fails.
Sample_Feature
Required when using HRD add-on kit
SoftwareVersion
Not Required
The TSO500S software version.
StartsFromFastq
Required
Set the value to TRUE or FALSE. To auto-launch from BCL files, set to FALSE. To auto-launch from FASTQ files after auto-launch of BCL Convert, set to TRUE.
SampleSheetRequested
Required
Set the value to TRUE or FALSE.
To auto-launch from BCL files, set to FALSE. To auto-launch from FASTQ files after auto-launch of BCL Convert, set to TRUE.
Sample_ID
Not Required
The same sample ID used in the Cloud_TSO500S_Data section.
ProjectName
Not Required
The BaseSpace project name.
LibraryName
Not Required
Combination of sample ID and index values in the following format: sampleID_Index_Index2
LibraryPrepKitName
Required
The Library Prep Kit used.
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_TSO500_Pipeline
Required
This value is a universal record number (URN) . The valid values are:
v2.6.0.8 (F2 compatible, includes HRD) urn:ilmn:ica:pipeline:142fb3af-f0aa-41f2-b043-f2913671e0b4#DRAGEN_TruSight_Oncology_500_v2_6_0_8 v2.6.2 urn:ilmn:ica:pipeline:b4dec62d-f3af-4dc3-8d15-6fe6c9a4df6c#DRAGEN_TruSight_Oncology_500_v2_6_2_4
BCLConvert_Pipeline
Required
urn:ilmn:ica:pipeline:a0778b16-f318-40df-ae04-95998e3a7564#BCL_Convert_v3_10_9_for_TSO500
SoftwareVersion
Required
Enter the IRM iapp software version 2.6.0-2v12ui
Enter trim This indicates that the BCL Convert software trims the specified adapter sequences from each read.
Indicates which lane corresponds to a given sample. Enter a single numeric value per row. Cannot be empty, i.e the analysis fails if the Lane column is present without a value in each row.
Required for HRD enriched samples.
For DNA samples that have undergone HRD enrichment, enter HRD in this column of the sample sheet. If the sample has not undergone HRD enrichment, leave the field empty.