*2.5. Quality Control and Quality Analysis*

HPV 16-positive (SiHa) and HPV-negative (water) controls were added at the DNA extraction step and carried through the PCR, library preparation and data analysis stages. Individual amplification products were assessed using a Bioanalyzer (Santa Clara, CA, USA). Quality control for library preparation included both controlling the library size using an Agilent Tapestation (Santa Clara, CA, USA) and determining the DNA concentration using the Qubit dsDNA High-Sensitivity Assay Kit (ThermoFisher, Waltham, MA, USA).

As a further quality control for analysis of the sequence data generated, a subset of 25 fastq files were sent to the International HPV Reference Laboratory in Karolinska, Sweden for independent bioinformatic analysis and sub-lineage identification.
