Scripts and nextstrain files for the following manuscript: Andrews KR, DD New, DS Gour, K Francetich, SA Minnich, BD Robison, CJ Hovde. 2023. Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town. Scientific Reports 13:7902. DOI:10.1038/s41598-023-34625-7 Also, check out the interactive phylogeny