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
FileFormatVersion
Yes
RunName
No
RunDescription
No
InstrumentType
No
NextSeq1000 or NextSeq2000
InstrumentPlatform
No
NextSeq1000 or NextSeq2000
Reads Sections
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
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
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
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
SoftwareVersion
Yes
Settings
ReferenceGenomeDir
Yes
Settings
For example, hg38_alt_aware.
MapAlignOutFormat
No
Settings
KeepFastq
No
Settings
Sample_ID
Yes
Data
Dragen DNA Amplicon
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
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)
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
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