NextSeq 1000/2000 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 Settings

FileFormatVersion

Yes

  

RunName

No

  

RunDescription

No

  

InstrumentType

No

NextSeq1000 or NextSeq2000

InstrumentPlatform

No

NextSeq1000 or NextSeq2000
Reads Sections

Parameter

Required

Instrument-Specific Settings

Read1Cycles

Yes

 

Read2Cycles

No

 

Index1Cycles

No

Required when sequencing more than one sample. Maximum is 10 cycles.

Index2Cycles

No

Required if using dual indexes for demultiplexing. Maximum is 10 cycles.

Sequencing Sections

Parameter

Required

Instrument-Specific Settings

LibraryPrepKits

No

Only one library prep kit is allowed.

In the NextSeq 1000/2000 Control Software v1.3 or later, the required custom recipe is automatically selected if one of the following kits is specified as the library prep kit.

• Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit
• Illumina Stranded mRNA Prep kit

Enter one of the following values.

• For Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, enter ILMNStrandedTotalRNA.
• For Illumina Stranded mRNA Prep kit, enter ILMNStrandedmRNA.

Application Sections

BCL Convert

Parameter

Required

Section

Instrument-Specific Requirements

AdapterRead1

No

Settings

Possible values are a concatenation from the set [A,C,T,G]. NextSeq 1000/2000 also allows a blank value. AdapterRead1 trims cycles by default. Value must be ≤ Read1Cycles.

AdapterRead2

No

Settings

Possible values are a concatenation from the set [A,C,T,G]. NextSeq 1000/2000 also allows a blank value. AdapterRead2 trims cycles by default. Value must be ≤ Read2Cycles.

BarcodeMistmatchesIndex1

No

Settings

  

BarcodeMismatchesIndex2

No

Settings

  

FastqCompressionFormat

No

Settings

  

OverrideCycles

No

Settings

  

SoftwareVersion

Yes

Settings

  

Sample_ID

Yes

Data

  

Index

No

Data

  

Index2

No

Data

  

Lane

No

Data

  
DRAGEN Enrichment

Parameter

Required

Section

Instrument-Specific Requirements

SoftwareVersion

Yes

Settings

  

ReferenceGenomeDir

Yes

Settings

For example, hg38_alt_aware.

BedFile

Yes

Settings

  

GermlineOrSomatic

Yes

Settings

  

KeepFastq

No

Settings

  

MapAlignOutFormat

No

Settings

  

AuxNoiseBaselineFile

No

Settings

 

Sample_ID

Yes

Data

  
DRAGEN Germline

Parameter

Required

Section

Instrument-Specific Requirements

SoftwareVersion

Yes

Settings

  

ReferenceGenomeDir

Yes

Settings

For example, hg38_alt_aware.

MapAlignOutFormat

No

Settings

  

KeepFastq

No

Settings

  

Sample_ID

Yes

Data

  
DRAGEN DNA Amplicon

Parameter

Required

Section

Instrument-Specific Requirements

SoftwareVersion

Yes

Settings

  

ReferenceGenomeDir

Yes

Settings

For example, hg38_alt_aware.

DnaBedFile

Yes

Settings

  

DnaGermlineOrSomatic

Yes

Settings

  

KeepFastq

No

Settings

  

MapAlignOutFormat

No

Settings

  

Sample_ID

Yes

Data

  

DnaOrRna

Yes

Data

 
DRAGEN RNA

Parameter

Required

Section

Instrument-Specific Requirements

SoftwareVersion

Yes

Settings

  

ReferenceGenomeDir

Yes

Settings

For example, hg38_alt_aware.

RnaGeneAnnotationFile

No

Settings

  

MapAlignOutFormat

No

Settings

  

KeepFastq

No

Settings

  

DifferentialExpressionEnable

No

Settings

  

Sample_ID

Yes

Data

  

Comparison<N>

No

Data

The N value reflects the comparison group of the samples.
DRAGEN Single Cell RNA (Single Cell Library Kit Types 1–6)

Parameter

Required

Section

Instrument-Specific Requirements

SoftwareVersion

Yes

Settings

  

ReferenceGenomeDir

Yes

Settings

For example, hg38_alt_aware.

RnaLibraryType

No

Settings

  

RnaGeneAnnotationFile

No

Settings

  

BarcodeRead

No

Settings

 

BarcodePosition

Yes

Settings

The value expected for Single Cell Library Kit Types 1–5 is different than the value for Single Cell Library Kit Types 6. Refer to Parameters for more information.

UmiPosition

Yes

Settings

  

BarcodeSequenceList

No

Settings

  

KeepFastq

No

Settings

  

MapAlignOutFormat

No

Settings

  

Sample_ID

Yes

Data