> 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/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000007753.md).

# Run Mode options for the NovaSeq X Series

The NovaSeq X Series offers several different options for setting up a sequencing run including Manual, Local, and Cloud options. Each of these will result in different downstream Secondary Analysis workflows and can be leveraged to support your analysis needs. All local analysis is performed using the onboard Dynamic Read Analysis for GENomics (DRAGEN) server.

![](/files/543TExpdicKS8yBtSoBm)

**Manual Mode (Generate BCLs Only)\***

* Can enter run configuration information directly in Control Software.
* No Local Secondary Analysis is performed.
* Can include an optional Sample Sheet during run setup, though this does not affect local Secondary Analysis.

**Import Sample sheet Mode**\*\*\*\*\*

(In NovaSeq X Control Software 1.3 this is called **Manual Mode (Import sample sheet for local analysis)**\*)

* Imports run setup information from a v2 Sample Sheet to quickly proceed through run setup.
* Preparing Sample Sheets through Run Planning on BaseSpace Sequence Hub is recommended, though a template Sample Sheet can also be used.
* Secondary analysis specified in the Sample Sheet using local DRAGEN is automatically started upon run completion.

**Local (On-Instrument)\***

* Can use the on-instrument Run Planning tool, a v2 Sample Sheet, or a networked computer to input run setup information.
* Secondary Analysis is performed using local DRAGEN on instrument and is automatically started upon run completion.

\*\*Cloud (\*\***BaseSpace Sequence Hub or Illumina BioInsight Platform Core (formerly, Illumina Connected Analytics (ICA)))**

* Use Run Planning setup in BaseSpace Sequence Hub.
* Secondary Analysis takes place in Cloud, analysis files will not be available on the instrument.

\*Using **Cloud Run Monitoring** or **Cloud Run Monitoring and Storage**

* To select *Cloud Run Monitoring* or *Cloud Run Monitoring and Storage* options during run setup, operator must sign into the NovaSeq X Series Control Software using the **Sign in to Illumina** **Cloud** option.
* This sign in option is available during Control Software initialization or by selecting the **Change account** button during run setup.
* If using local instrument login only, Cloud Options will not be available during run setup.

For further information, see:

Plan a Manual Sequencing Run: [How to plan a Manual Mode NovaSeq X Series run](/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000008540.md)

Plan a Local Sequencing Run: [How to plan a Local sequencing run on the NovaSeq X Series](/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000008528.md)

Plan a Cloud Sequencing Run: [Plan a NovaSeq X Series Run in BaseSpace Sequence Hub](https://help.basespace.illumina.com/sequence/plan-runs/multi-analysis-planned-run)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7753), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007753%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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