> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/nextseq-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000002450.md).

# 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.

![](/files/WHbP3VMELCx0PaQ4vJiO)

**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](https://support.illumina.com/sequencing/sequencing_instruments/nextseq-1000-2000/product-files.html) and follow the guidance in the Sample Sheet v2 Settings section of the [NextSeq 1000/2000 Product Documentation](https://sapac.support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html).
* 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.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2450), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002450%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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