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

Parameter

Required

Instrument-Specific Requirements

FileFormatVersion

Yes

  

RunName

Yes

  

RunDescription

No

  

InstrumentType

No

 

InstrumentPlatform

No

Enter NovaSeqXSeries for NovaSeq X Series.

Custom_*

No

  
Reads Sections

Parameter

Required

Instrument-Specific Requirements

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

Parameter

Required

Instrument-Specific Requirements

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

Parameter

Required

Section

Instrument-Specific Requirements

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:

• The AdapterRead2 field is placed in the Data section of the Sample Sheet
• No adapter trimming is desired for the sample.

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

Parameter

Required

Section

Instrument-Specific Requirements

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

Parameter

Required

Section

Instrument-Specific Requirements

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

Parameter

Required

Section

Instrument-Specific Requirements

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

Parameter

Required

Section

Instrument-Specific Requirements

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

Parameter

Required

Section

Instrument-Specific Requirements

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