Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"

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)