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SARS-CoV-2 genomic epidemiology at a public university in the United States

This repository holds information related to our paper on SARS-CoV-2 genomic epidemiology in southeastern Michigan in Fall 2020. Below is a map of the repository structure.

Overview

project
|- README          # The top level description of content.
|
|- data  
|  |- reference/  # Reference files: publicly available data on COVID-19 cases in Michigan and the University of Michigan. GISAID accessions used in this study.
|- scripts/       # Code for consensus genome assembly and core phylogenetic analyses.

Notes

Consensus genome sequences used in this paper are available on GISAID, as listed in the supplemental tables.

Contact

If you have questions, please contact the Lauring Lab.