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

Headers 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