@misc{Crits-Christoph_A-2024_186390,
title = {Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"},
author = {Crits-Christoph, A. and Levy, J. and Pekar, J. and Goldstein, S. and Singh, R. and Hensel, Z. and Gangavarapu, K. and Rogers, M. and Moshiri, N. and Garry, R. and Holmes, E. and Koopmans, M. and Lemey, P. and Peacock, T. and Popescu, S. and Rambaut, A. and Robertson, D. and Suchard, M. and Wertheim, J. and Rasmussen, A. and Worobey, M. and Andersen, K. and Débarre, F.},
month = {jun},
year = {2024},
abstract = {This repository provides data, sequences, and analyses of the metagenomic detection of mammalian wildlife at the Huanan Market in early 2020. **Article sections:** - (R1): SARS-CoV-2 genetic diversity linked to the Huanan market is consistent with market emergence - (R2): Increased High SARS-CoV-2 positivity rate in and near a wildlife stall in the Huanan market - (R3): Mammalian wildlife species detected in five SARS-CoV-2 positive samples from a wildlife stall and in other wildlife stalls - (R4): Wildlife stalls and SARS-CoV-2 positive samples contain other mammalian viruses associated with the animal trade - (R5): Reconstruction of mitochondrial genotypes of potential intermediate host species of SARS-CoV-2 within the Huanan market ## Contents by folder - `metadata/`: sample and species metadata (R) - `mitochondrial_mappings/`: Read mapping counts and covered bases (breadth) for animal mtDNA. (R3, R5) - `mitochondrial_genotypes/`: Animal mtDNA consensus genotypes and SNV VCFs. (R3, R5) - `sars2_mappings/`: identification and quantification of SARS-CoV-2 reads. (R1, R2) - `sars2_phylogenetics/`: SARS-CoV-2 phylogeny. (R1) - `viruses`: identification and quantification of other viruses in the market. (R4) - `correlations/`: computations of correlations between viruses and animals (R3) - `fastq_processing/`: code for sample (pre)processing (R) - `figs/`: directory where figure outputs are stored (R) - `figures_R/`: R code to generate figures (R) - `summary_and_tables/`: Supplementary tables (R)},
journal = {Zenodo},
publisher = {Zenodo},
url = {https://doi.org/10.5281/zenodo.12571327},
}
