NovaSeq X Series Settings
For descriptions of each field, including the specific requirements and if the expected value is an integer or string, refer to Parameters.
Standalone Sections
Header Sections
FileFormatVersion
Yes
RunName
Yes
RunDescription
No
InstrumentType
No
InstrumentPlatform
No
Enter NovaSeqXSeries for NovaSeq X Series.
Custom_*
No
Reads Sections
Read1Cycles
Yes
Read2Cycles
No¹
Index1Cycles
No¹
Value must be in the 6–12 range for the following run types:
Runs planned in the cloud
Runs planned locally using import sample sheet
Manual runs with local analysis
The total number of read cycles and index cycles cannot exceed the number of cycles specified by the reagent kit. The index cycle limit applies to cycles used as an index, not UMI cycles or trimmed reads.
Index2Cycles
No¹
Value must be in the 6–12 range for the following run types
Runs planned in the cloud
Runs planned locally using import sample sheet
Manual runs with local analysis
The total number of read cycles and index cycles cannot exceed the number of cycles specified by the reagent kit. The index cycle limit applies to cycles used as an index, not UMI cycles or trimmed reads.
¹ Depending on the run or library prep kit, this parameter might be required.
Sequencing Sections
CustomRead1Primer
No¹
CustomRead2Primer
No¹
CustomIndex1Primer
No¹
CustomIndex2Primer
No¹
¹ Depending on the run or library prep kit, this parameter might be required.
Application Sections
For NovaSeq X Series, there is a limit of four application sections for onboard analysis or eight application sections for cloud analysis.
BCL Convert
SoftwareVersion
Yes
Settings
FastqCompressionFormat
Yes
Settings
Supported values are gzip or dragen.
To use DRAGEN Illumina Complete Long Reads WGS (ICLR WGS), the recommended value is gzip.
AdapterRead1
No
Data
Possible values are a concatenation from the set [A,C,T,G]. NovaSeq X Series also allows na.
A value of na (case insensitive) must be used if both the following statements are accurate:
The AdapterRead1 field is placed in the Data section of the Sample Sheet
No adapter trimming is desired for the sample.
AdapterRead2
No
Data
Possible values are a concatenation from the set [A,C,T,G]. NovaSeq X Series also allows na.
A value of na (case insensitive) must be used if both the following statements are accurate:
No adapter trimming is desired for the sample.
The AdapterRead2 field is placed in the Data section of the Sample Sheet
BarcodeMismatchesIndex1
No
Data
NovaSeq X Series allows the value na in addition to the values 0, 1, or 2.
Enter a value of na if:
BarcodeMismatchesIndex1 exists in the Data section of the Sample Sheet, and
OverrideCycles exist in the data section, and
Index 1 is masked out for the sample in the OverrideCycles
BarcodeMismatchesIndex2
No
Data
NovaSeq X Series allows the value na in addition to the values 0, 1, or 2.
Enter a value of na if:
BarcodeMismatchesIndex2 exists in the Data section of the Sample Sheet, and
OverrideCycles exist in the data section, and
Index 2 is masked out for the sample in the OverrideCycles
OverrideCycles
No
Data
OverrideCycles example:
Y151;I8N2;N2I8;Y151
For DRAGEN ICLR WGS, use the following guidelines:
When using only DRAGEN BCL Convert and DRAGEN ICLR WGS, enter
Y151;Y151.When using DRAGEN BCL Convert, DRAGEN ICLR WGS, and additional apps, enter
Y151;NX;NX;Y151,replacing X with the correct index length.
Sample_ID
Yes
Data
Lane
Yes
Data
For NovaSeq X, values must be in the range of lanes specified in RunInfo.xml:
1.5B flow cell: 1–2
10B flow cell: 1–8
25B flow cell: 1–8
Index
Yes
Data
For NovaSeq X, a value of na must be used if no indexes are specified in OverrideCycles for a sample.
When using DRAGEN ICLR WGS, leave blank.
Index2
No
Data
Always write index sequences in the forward orientation. BCL Convert handles index orientation.
When using DRAGEN ICLR WGS, leave blank.
DRAGEN Enrichment
SoftwareVersion
Yes
Settings
AppVersion
Yes
Settings
KeepFastQ
Yes
Settings
MapAlignOutFormat
Yes
Settings
If MapAlignOutFormat is set to none, VariantCallingMode cannot be none for any sample.
ReferenceGenomeDir
Yes
Data
Bedfile
Conditionally required
Data
Only required if VariantCallingMode is not None.
Must include the prefix DragenEnrichment/ before the BED file name.
The value must be na if BedFile is placed in the Data section and VariantCallingMode is set to None.
GermlineOrSomatic
Yes
Data
AuxNoiseBaselineFile
No
Data
The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample.
AuxCnvPanelOfNormalsFile
Conditionally required
Data
Optional if VariantCallingMode is AllVariantCallers.
The value must be na if AuxCnvPanelOfNormalsFile is placed in the Data section and no AuxCnvPanelOfNormalsFile is provided for the sample.
VariantCallingMode
Yes
Data
Sample_ID
Yes
Data
DRAGEN Germline
SoftwareVersion
Yes
Settings
AppVersion
Yes
Settings
KeepFastQ
Yes
Settings
MapAlignOutFormat
Yes
Settings
If MapAlignOutFormat is set to none, VariantCallingMode cannot be none for any sample.
ReferenceGenomeDir
Yes
Data
VariantCallingMode
Yes
Data
QcCoverage1BedFile
No
Data
Only supported for v4.1.23 and later.
QcCoverage2BedFile
No
Data
Only supported for v4.1.23 and later.
QcCoverage3BedFile
No
Data
Only supported for v4.1.23 and later.
QcCrossContaminationVcfFile
No
Data
Only supported for v4.1.23 and later.
Sample_ID
Yes
Data
DRAGEN RNA
SoftwareVersion
Yes
Settings
AppVersion
Yes
Settings
MapAlignOutFormat
Yes
Settings
For the DRAGEN RNA application, selecting none is not allowed if RnaPipelineMode is set to MapAlign for any sample.
KeepFastQ
Yes
Settings
DifferentialExpressionEnable
No
Settings
ReferenceGenomeDir
Yes
Data
RnaGeneAnnotationFile
No
Data
RnaPipelineMode
Yes
Data
DownSampleNumReads
No
Data
Sample_ID
Yes
Data
Comparison1
No
Data
Comparison2
No
Data
Comparison3
No
Data
Comparison4
No
Data
Comparison5
No
Data
DRAGEN Somatic
SoftwareVersion
Yes
Settings
AppVersion
Yes
Settings
KeepFastQ
Yes
Settings
MapAlignOutFormat
Yes
Settings
ReferenceGenomeDir
Yes
Data
AuxNoiseBaselineFile
No
Data
AuxSvNoiseBaselineFile
No
Data
AuxCnvPopBAlleleVcfFile
No
Data
AuxGermlineTaggingFile
No
Data
VariantCallingMode
Yes
Data
Sample_ID
Yes
Data
DRAGEN Methylation
SoftwareVersion
Yes
Settings
AppVersion
Yes
Settings
KeepFastQ
Yes
Settings
MapAlignOutFormat
Yes
Settings
UsesTaps
Yes
Settings
ReferenceGenomeDir
Yes
Data
MethylationProtocol
No
Data
Sample_ID
No
Data
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