What is the PhiX Control v3 Library and what is its function in Illumina Next Generation Sequencing

The PhiX Control v3 Library (commonly referred to as PhiX, FC-110-3001) is derived from the small, well-characterized bacteriophage genome, PhiX. It is a concentrated Illumina library (10 nM in 10 µl) that has an average size of 500 bp and consists of balanced base composition at ~45% GC and ~55% AT.

Calibration Control

The PhiX Control v3 Library can be sequenced alone and serves as a calibration control for:

• Cross talk matrix generation

• Phasing and prephasing calculations

• Examining the overall performance of Illumina sequencing platforms

For detailed information, see:

• PhiX loading concentrations for validation runs on Illumina sequencing platforms

• How to set up the sample sheet for a PhiX validation run on the MiSeq system using Illumina Experiment Manager

• How to set up a PhiX validation run on the NextSeq 500/550 in manual mode

• How to set up a PhiX validation run on the NextSeq 500/550 system using BaseSpace Hub Prep tab

• How to set up a PhiX validation run on the NextSeq 1000/2000 sequencing platform

• How to set up a PhiX validation run on the NovaSeq 6000 sequencing platform

• Local Run Manager: How to set up a PhiX validation run

Run Quality Monitor

Due to its balanced nucleotide composition, the PhiX Control v3 Library is also an ideal sequencing control (typically with ≥ 1% spike-in) for run quality monitoring; eg, cluster generation, sequencing, and alignment.

Color Balancing

For low diversity libraries, the PhiX Control v3 Library provides balanced fluorescent signals at each cycle to improve the overall run quality. For detailed information, see:

• What is nucleotide diversity and why is it important?

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