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      • 2025
        • 7.33.0 - Shared BCL Convert Section
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      • 2024
        • 7.29.0 - Improved Analysis Error Reporting
        • 7.28.0 - MiSeq i100 Support
        • 7.27.0 - App Store Upgrade
        • 7.26.0 - Prep Tab Obsolescence Notification
        • 7.25.0 - Project Column in the Analysis Files Tab
        • 7.24.0 - Requeue Improvements
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        • 7.22.0 - Analysis Autolaunch for NovaSeq X Manual Mode Runs
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        • 7.18.0 - Custom Kit Deletion
      • 2023
        • 7.17.0 - Deletion of Biosample Default Projects
        • 7.16.0 - Transfer of NovaSeq X Runs
        • 7.15.0 - Compatibility Filtering in Run Planning
        • 7.14.0 - Native App Engine Update
        • 7.13.0 - Sharing for NovaSeq X Runs and Analyses
        • 7.12.0 - Combined New and Classic Modes
        • 7.11.0 - NovaSeq X Analysis Requeue
        • 7.10.0 - NovaSeq X Analysis Autolaunch Improvements
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        • 7.8.0 - Performance Improvements
      • 2022
        • 7.7.0 - NovaSeqX Support
        • 7.6.0 - Custom Configuration Files in Microarray Analysis Setup
        • 7.5.0 - Performance Enhancements
        • 7.4.0 - Run Planning Enhancements
        • 7.3.0 - Improve App Launch Performance
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        • 7.1.0 - FastQ Related Fixes and Performance Improvements
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        • 6.17.0 - Preliminary ICA Integration
      • 2021
        • 6.16.0
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        • 6.14.0
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      • 2020
        • 6.4.0
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        • 5.46.0
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      • 2019
        • 5.41.0
        • 5.40.0
        • 5.39.0
        • 5.38.0
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        • 5.36.0
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        • 5.34.0
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        • 5.30.0
      • 2018
        • 5.29.0
        • 5.28.0
        • 5.27.0
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        • 5.24.0
        • 5.23.0
        • 5.22.0
        • 5.21.1
        • 5.21.0
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        • 5.16.0
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        • 5.14.0
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        • 5.11.0
      • 2017
        • 5.10.0
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      • 2016
        • 4.14.0
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      • 2015
        • 3.23.2
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  1. Sequence
  2. Plan Runs
  3. Prep Tab

Plan Run Using Prep Tab

PreviousPool LibrariesNextNeo Prep

Last updated 3 months ago

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The Prep tab is deprecated and no longer available. For run planning and sequencer integration, see the section.

Plan Runs

  1. On the Plan Run page, click the Select Instrument drop-down arrow, and select a sequencing system, either MiniSeq or NextSeq.

  2. In the Name field, enter a name for the sequencing run.

  3. [Optional] In the Reagent Barcode field, enter the barcode ID of the reagent kit used for the run. Entering the barcode ID links the reagent kit to the run.

  4. [Optional] Select Use Custom Primer options:

    • R1 — Use custom primer for Read 1.

    • R2 — Use custom primer for Read 2.

  5. Select a read type, either Single Read or Paired End.

  6. Enter the number of cycles for each read in the sequencing run:

    • Read 1 Cycles — Enter a value up to 151 cycles.

    • Read 2 Cycles — Enter a value up to 151 cycles. This value is typically the same number of cycles as Read 1.

  7. Review the indexing scheme for the run. To make changes, override the defaults as follows.

    1. Select the Override default indexing scheme checkbox.

    2. Select an indexing scheme:

      • Single Index — Performs a run with 1 index read.

      • Dual Index — Performs a run with 2 index reads.

      • No Index — Performs a non-indexed run.

    3. Enter the number of cycles for each index read*:

      • Index 1 Cycles — Enter the number of cycles required for the Index 1 (i7) primer.

      • Index 2 Cycles — Enter the number of cycles required for the Index 2 (i5) primer.

  8. Make sure that a pool is present.

  9. Select 1 of the following buttons to continue:

    • Sequence — The run appears on the Planned Runs list with a status of Ready. The run becomes available from the control software of your sequencing system.

    • Save and Continue Later — The run appears on the Planned Runs list with a status of Planning. When you are ready to sequence, select the checkbox for the run and select Sequence. The run then becomes available from the control software of your sequencing system.

*Indexing is required when sequencing multiple libraries.

Run Planning