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:

  • BSSH Run Planning > Secondary Analysis "Local Mode" is selected > 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

• Control Software Run Setup Setting: Cloud

• Run is setup in BSSH Run Planning > Select Secondary Analysis option "Local Mode" > Login to BaseSpace and start run with the planned run

• 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 > Select Secondary Analysis option "BaseSpace" > Login to BaseSpace and start run with the planned run

• Secondary DRAGEN analysis is performed in the Cloud and No local FASTQ files are generated

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 and FASTQ files are desired in BaseSpace, a Sample sheet is required with the "BaseSpace" option selected for Secondary Analysis in BSSH Run Planning.

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