Shotgun Metagenomics of the Upper Respiratory Tract
Viral DNA was extracted using the Extracta Kit and quantified with a Qubit fluorometer. Library preparation used Illumina Nextera and sequencing was done on the Illumina NextSeq 550 platform, yielding ~39.7 million read pairs. Reads were trimmed with fastp, assembled with MEGAHIT, and annotated using Kraken2.