Local Run Manager: How to set up a PhiX validation run on the iSeq, MiniSeq, or MiSeq


A PhiX validation run confirms proper hardware and software performance of the instrument. The Illumina PhiX control library is a well-balanced genome with relatively equal representation of A, T, G, and C nucleotides. PhiX lacks an index and is not an appropriate tool for assessing Index Read performance.

To set up a PhiX validation run on the iSeq, MiniSeq, or MiSeq systems using the on-instrument-installed Local Run Manager software:

  1. Launch the Chromium browser and enter http://localhost in the address bar. If User Management is enabled, the login page will appear, requiring you to enter the user ID and password.
  2. Select Create Run, and choose Resequencing from the drop-down list.

  3. Enter the following values in the highlighted fields:
    • Run Name: PhiX validation run
    • Library Prep Kit: TruSeq LT
    • Index Reads: 0 (Note: PhiX is unindexed and selecting 1 or 2 index reads can cause the run to terminate prematurely)
    • Read Type: Paired End
    • Read Length: Enter at least 26 cycles for each read
  4. Keep default values in the Module-Specific Settings field.

  5. Scroll to the bottom of the Create Run page. In the Import Samples table, type PhiX in the Sample ID field.
  6. In the Genome Folder field, select PhiX from the species column.

  7. Select Save Run.

  8. Close the browser window and return to the MiniSeq Control Software.
  9. Select PhiX validation run from the available runs list and proceed to sequencing.

    For more information on preparing PhiX libraries for sequencing on the MiniSeq & MiSeq platforms, consult the MiniSeq System Denature and Dilute Libraries Guide and the MiSeq System Denature and Dilute Libraries Guide.