Sample Sheets
Overview
A sample sheet is required for each analysis with the pipeline. A sample sheet is a comma-separated value (*.csv) file format used by Illumina instruments, platforms, and analysis pipelines to store settings and data for sequencing and analysis. The pipeline is compatible with the sample sheet v2. For general information on the sample sheet v2, refer to Illumina Connected Software Sample Sheet.
A full sample sheet includes multiple sections, including a [BCLConvert_Settings] section with a list of samples and their index sequences, along with additional information required to run the pipeline in the [{app}_Data] section. For example, the Library Prep Kit is a required field in the sample sheet for the DRAGEN Heme WGS Tumor Only Pipeline. Both Illumina library prep kits or custom library prep kits are supported.
On the other hand, the DRAGEN Solid WTS Tumor Normal Pipeline may only required a minimal sample sheet with only [Header] section and a [TN_Data] section when starting the analysis from FASTQ. This partial sample sheet is not valid when starting analysis from a run folder.
When running analysis on a standalone DRAGEN server or ICA, a valid sample sheet can be created by:
BaseSpace Run Planner (preferred), see BaseSpace Run Planner for details.
Downloading and modifying a sample sheet template following the requirements, see Requirements for details.
When running analysis on a standalone DRAGEN server or on ICA, a minimal sample sheet for starting from FASTQ, BAM or CRAM can be created by:
Modify a sample sheet template following the requirements, see product specific templates for more information.
Note: A minimal sample sheet may be invalid for other purposes. It is always advisable to use a valid sample sheet generated from the BaseSpace Run Planner.
The Run Planning section of this guide is available for specific instructions to plan a run and set up a valid sample sheet for the pipeline when supported.
New Sample Sheet options available in DRAGEN 4.4+ release
Forward orientation for index2
With v2 sample sheet, and DRAGEN 4.4+, it is now required for users to specify index2 orientation in forward orientation only. For additional information, see Index Orientation Guide.
SoftwareVersion
Required
if SoftwareVersion >=4.4, index2 orientation must be forward; Otherwise, legacy behavior is supported
RunInfoIndex2ReverseComplement
Optional
Allowed values Y/N. if SoftwareVersion >=4.4; paired presence required with Index2ColumnReverseComplement. This value overrides the RunInfo.xml isReverseComplement = Y/N flag for index2 orientation in case of conflict.
Index2ColumnReverseComplement
Optional
Allowed Values Y/N. If softwareVersion >=4.4; paired presence required with RunInfoIndex2ReverseComplement. This value indicates whether the index2 column sequence is reverse complement or not.
Summary of Valid Settings for Index Orientation
As indicated in the following Table, the index2 orientation is always Forward orientation for simplicity. The two new flags introduced are especially useful when custom LPKs are used and when a consistent index2 orientation is desired for all run folders. The IndexOrientation field is present from BaseSpace run planner generated sample sheet, and indicates that the sample sheet index2/i5 sequences are in Forward orientation.
Look up table for index2 orientations in DRAGEN 4.4+
Bcl-convert SoftwareVersion must be >=4.4.
* indicates the situation where the IsReverseComplement flag in the RunInfo.xml is overriden by the RunInfoIndex2ReverseComplement value. NA means that IsReverseComplement flag for the index2 is not present in the RunInfo.xml file.
** indicates that legacy run folders may use the two paired flags to ensure that index2 Forward orientation is consistently applied.
NovaSeq 6000
Forward
N**
N**
NA
Forward
When SbsConsumableVersion <3
Forward
Y**
N**
NA
Forward
When SbsConsumableVersion >=3
NovaSeq 6000Dx
Forward
Y
N
Y
Forward
When non-SP flow cell is used
Forward
Y
N
N*
Forward
When SP flow cell is used and control software is <2.4
NovaSeq X
Forward
Y
N
N
Forward
Summary of Legacy Settings for index2 orientations
For backward compatibility, when the bcl-convert version specified is less than 4.4, the index2 orientation may vary depending on the instrument. In BaseSpaces run planner generated sample sheet, the IndexOrientation may still indicate Forward, but it is ignored in this situation.
Look up table for index2 orientations in earlier DRAGEN versions
Bcl-convert SoftwareVersion must be <4.4.
*indicates the situation where the IsReverseComplement flag in the RunInfo.xml is different depending on the control software version.
NovaSeq 6000
NA
Forward
When SbsConsumableVersion <3
NA
Reverse
When SbsConsumableVersion >=3
NovaSeq 6000Dx
Y
Forward
When non-SP flow cell is used
Y*
Forward
When SP flow cell is used and control software is >2.4
N*
Reverse
When SP flow cell is used and control software is <2.4
NovaSeq X
Y
Forward
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