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* 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:

• BSSH Run Planning > Local Mode > Export Sample sheet.

• v2 Sample sheet template NextSeq 1000/2000 Sequencing System Product Files and follow the guidance in the Sample Sheet v2 Settings section of the NextSeq 1000/2000 Product Documentation.

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

Option 2: Hybrid (Local + Cloud) Run Mode

• Run is setup in BSSH Run Planning.

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

Option 3: Cloud Run Mode

• Run is setup in BSSH Run Planning.

• Secondary DRAGEN analysis is performed in the Cloud.

Option 4: Standalone Mode

• 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).

If using Local, Hybrid, or Standalone Mode, and in the settings Proactive, Run Monitoring and Storage is selected, it will send all the run data to BaseSpace and will generate FASTQ files if the Sample Sheet is included.

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