Submitted version, January 22, 2024

The version here tagged of the repository is the version with all codes and pipelines to reproduce the analysis and figures published in the paper entitled: "Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the United States" submitted to Cell Reports/Cell Systems.

A preprint version of the following version is available here: https://www.medrxiv.org/content/10.1101/2023.11.07.23298178v2

preprint DOI: https://doi.org/10.1101/2023.11.07.23298178

Zenodo DOI: https://doi.org/10.5281/zenodo.11074203