# How to plan a Local sequencing run on the NovaSeq X Series **Background** The NovaSeq X allows users to setup sequencing runs using Local or Cloud Run Planning, importing a Sample Sheet, or Manual mode. See the following steps to setup a sequencing run using Local Run Planning options. For more information on Run Modes, see Knowledge Article [Run Mode options for the NovaSeq X Series](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000007753) To setup a Manual Mode Run, refer to Knowledge Article [Planning a Manual Mode Run on NovaSeq X Series](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000008540) for more information. **Using Local Run Planning** 1. Select the instrument icon at the bottom of the NovaSeq X Series Control Software to open the global navigation menu. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-a8abdbe9dd6f0e112cbc96e3ee8667d63a3fa588%2Fimage1.png?alt=media) 2. Select **Runs**, then navigate to the Planned tab and select **Create Run**. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-404220ccdc7cd739e093a99c67e8c1d8a8b68b77%2Fimage2.png?alt=media) 3. In **Run Settings**, enter the applicable options: ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-c662ef026e4a30c1b6765d5214190491ccc96f91%2Fimage3.png?alt=media) **Run Name**: A name to identify the current run (maximum of 255 alphanumeric characters, spaces, periods, dashes, and underscores are allowed). **Run Description**: \[*Optional* and cannot contain asterisks, brackets, or commas]. **Generate FastQC metrics**: If enabled, the analysis pipeline generates FastQC metrics. **Read Lengths**: * Read 1 — Enter the cycles number. * Index 1 — length of the index read for Index 1. * Index 2 — length of the index read for Index 2. * Read 2 — Enter the cycles number. All Read Length fields must have a numerical value input. To skip a Read, input 0 for the number of cycles for that Read. ***Note for NovaSeq X Control Software v1.3 and above:*** **Library tube ID** is renamed as **Sample Container ID**.\[*Optional* and is on the label of the library tube strip]. Select **Next**. 4. In **Configuration**, enter: ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-6734679d9520a7e9b42ad8fd77a44eca7c180e43%2Fimage4.png?alt=media) **Applications**: Select the desired analysis applications **Description**: \[*Optional*] **Library Prep Kit**: Select a kit **Index Adapter Kit**: Select a kit For information on adding custom library prep and index adapter kits, refer to [Import Custom Library Prep and Index Adapter Kits.](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/AddCustomKits.htm) Select **Next**. 5. Input the sample and indexes information (i5 indexes must be entered in the forward orientation). ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-60a8150c167f07997ac781d732f3b8d0763fea1c%2Fimage5.png?alt=media) To import samples, select Download template and fill out the Sample ID and Index information, then select Import Samples and import the filled out template file. Select **Next**. 6. Review the run configuration. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-0f9f363766ad6bd2cc340a369d24d09de43115eb%2Fimage6.png?alt=media) **Note for NovaSeq X Control Software 1.2.2 and below**: Up to 4 DRAGEN applications can be selected for on-board local analysis (1 BCL + 3 additional DRAGEN apps). Up to 8 DRAGEN applications can be selected for cloud analysis (1 BCL + 7 additional DRAGEN apps). Enter up to 8 Library Prep and Index Adapter kits combinations, per App (DRAGEN App + genome) configuration. To enable multiple DRAGEN analysis configurations per run, select "Add Another Configuration". ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-014d7c4ca2dd9e2de2ec9c6addf63b48d0b58c0e%2Fimage7.png?alt=media) **Note for NovaSeq X Control Software 1.3 and above:** Up to 12 DRAGEN applications plus 1 BCL Convert application can be selected for both on-board and cloud analysis. Enter up to 32 Library Prep and Index Adapter kits combinations, per App (DRAGEN App + genome) configuration. To enable multiple DRAGEN analysis configurations per run, select "Add Another Configuration". * ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-7949672f1066ab32125b4634f6ab17140e36f1fc%2Fimage8.png?alt=media) * **Note**:One sample can be loaded in multiple lanes (Sample 5 in Lane 1 and 2), but you cannot include the same sample for two different App Configuration. 7. Select **Save As Planned** to complete the run details and plan for sequencing. 8. In the global navigation menu, select **Start** and then **Sequencing** in Control Software home screen. 9. Select the desired side. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d81ecab74792e966ffa86721ce4bb2642c8265df%2Fimage9.png?alt=media) 10. Select the current planned run. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-33da154a9d2df06f797e67ada103d5995e294422%2Fimage10.png?alt=media) **Note:** To change account or sign in the BaseSpace account select Change account button 11. Select **Review** to check the run configuration. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-b7f842cbb8394d20c2c917b01cfaa45d62a9386a%2Fimage11.png?alt=media) Using custom sequencing primer: ***NovaSeq X Control Software v1.2.2 and below:*** Select the appropriate custom primer recipe XML file. ***NovaSeq X Control Software v1.3 and above:*** Select the applicable custom primer checkboxes. Uploading a custom recipe disables the custom primer checkboxes. For more information on custom primers, refer to [Custom Primers](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/CustomPrimers.htm). Confirm the output folder before proceeding. For information on selecting the applicable Output folder, see article [How to configure External Storage locations on the NovaSeq X/X Plus](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-reference_material-list/000007775) 12. Load the consumables and start the run. After sequencing, Secondary Analysis starts with local DRAGEN on instrument. For Additional Information See: [*Set Up Secondary Analysis*](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/SecondaryAnalysisSetup.htm) For Additional Information See: [NovaSeq X Plus Product Documentation, Plan a Local Sequencing Run](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/PlanaRun.htm) \ \ \
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