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Run mode options for the NextSeq 1000/2000

The NextSeq 1000/2000 has four run setup options. Cloud refers to BaseSpace Sequence Hub (BSSH). Any BSSH subscription type can use either Cloud or Hybrid Run Mode.

Option 1: Local Run Mode* Control Software Run Setup Setting: Local

  • Run is setup with a v2 sample sheet imported at the time of run start. If selecting local mode, a sample sheet is required. A sample sheet can be obtained from one of the following options:

  • Secondary analysis is performed on local DRAGEN Bio-IT FPGA.

Option 2: Hybrid (Local + Cloud) Run Mode

  • Control Software Run Setup Setting: Cloud

  • Run is setup in BSSH Run Planning.

  • Secondary analysis is performed on local DRAGEN Bio-IT FPGA.

Option 3: Cloud Run Mode

  • Control Software Run Setup Setting: Cloud

  • Run is setup in BSSH Run Planning.

  • Secondary DRAGEN analysis is performed in the Cloud.

Option 4: Standalone Mode

  • Control Software Run Setup Setting: Local

  • Run is setup in the Control Software.

  • No Secondary Analysis occurs on board.

  • If sending data to BSSH for Proactive, Run Monitoring, and Storage a Sample sheet is required for BSSH analysis (the version of the sample sheet does not matter).

When using Local, Hybrid, or Standalone Mode:

  • If the setting "Proactive, Run Monitoring and Storage" is selected and the Sample Sheet was included and created in BSSH Run Planning with the Secondary Analysis set to "BaseSpace", it will send all the run data to BaseSpace and will generate FASTQ files.

  • If a Sample Sheet is not included, the run status will be "Needs Attention".

  • If the Sample Sheet is included but the Secondary Analysis is set to "Local", no FASTQ files will be generated.

For any feedback or questions regarding this article (Illumina Knowledge Article #2450), contact Illumina Technical Support [email protected].

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