BCL conversion for supplementary analysis

Generating FASTQs using BCL Convert

FASTQs can be generated using TSO 500 or BCL Convert. When starting analysis from TSO 500, follow the DRAGEN TSO 500 v2.6 guide, and go to Supplemental CNV analysis using DRAGEN Enrichment for additional analysis. When generating FASTQs with BCL Convert, the following [BCLConvert_Settings] and [BCLConvert_Data] should be used to generate FASTQs with BCL Convert for subsequent launch of TSO 500 and DRAGEN Enrichment from FASTQ. BCL Convert pipeline versions 3.9.10 and 4.4.10 were tested upstream of TSO 500 and DRAGEN Enrichment analyses, and all BCL Convert versions 3.9.10 and newer are expected to be compatible. For more information on launching BCL Convert, see the BCL Conversion support page.

[BCLConvert_Settings]

Sample Parameter	Required	Details
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	Enter trim This indicates that the BCL Convert software trims the specified adapter sequences from each read.
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.
OverrideCycles	Required	U7N1Y93;I10;I10;U7N1Y93

[BCLConvert_Data]

Sample Parameter	Required	Details
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	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.

For all other sample sheet requirements (sample IDs, indexes, TSO 500 data sections, and launching TSO 500 from FASTQ), refer to Sample Sheet Requirements.

Sample sheet templates

TSO 500 sample sheet templates are available on Sample Sheet Templates. When starting form BCL Convert, [TSO500_Settings] and [TSO500_Data] are not required.