How to set up a PhiX validation run with Local Run Manager

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.

PhiX validation runs can be set up with Local Run Manager on instruments with the Local Run Manager software suite bundled for on-instrument use. These instruments are the iSeq 100; MiSeq with MiSeq Control Software v3 and v4; NextSeq 500/550 with Control Software v4; and MiniSeq. Note that MiniSeq instruments with MiniSeq Control Software v1 have Local Run Manager v1.3, while MiniSeq instruments with Control Software v2 have Local Run Manager v2. Instruments running MiSeq Control Software v3 have Local Run Manager v2 and MiSeq Control Software v4 has Local Run Manager v3.

1. Launch the Chromium browser and enter http://localhost in the address bar. If User Management is enabled in Local Run Manager v2 or v3, the login page will appear, requiring you to enter the user ID and password. If User Management is disabled, the dashboard will appear. Version 1.3 of Local Run Manager for MiniSeq always requires a login.
2. Select Create Run and choose Generate FastQ from the drop-down list.
3. Enter the following values in the highlighted fields:

• Run Name: PhiX validation run

• Library Prep Kit: Custom

• 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 (or follow Illumina Support guidance on the number of 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. Select Save Run.

7. Close the browser window and return to the instrument Control Software.

8. Select the Local Run Manager run setup option and then select ‘PhiX validation run’ from the list of available runs and proceed to sequencing.

For any feedback or questions regarding this article (Illumina Knowledge Article #1318), contact Illumina Technical Support [e-mail].