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:
- 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.
- Select Create Run, and choose Resequencing from the drop-down list.
- 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
- Keep default values in the Module-Specific Settings field.
- Scroll to the bottom of the Create Run page. In the Import Samples table, type PhiX in the Sample ID field.
- In the Genome Folder field, select PhiX from the species column.
- Select Save Run.
- Close the browser window and return to the MiniSeq Control Software.
- 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.