Individual-Bat-Virome

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Individual-Bat-Virome

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Codes and data for the manuscript "Wang et al. (2022) The viromes of individual Chiroptera reveal the co-infection, spillover and emergence risk of potential zoonotic viruses"

Individual-Bat-Virome 최신버젼 다운로드

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# Individual Bat Virome

This repository contains codes and data of the manuscript "Wang et al. (2022) The viromes of individual Chiroptera reveal the co-infection, spillover and emergence risk of potential zoonotic viruses".

## Viral genome sequences

We are still uploading raw sequences and assembled genome sequences to NCBI. We will provide accession numbers of these data ASAP. Currently, genome sequences of viruses, as well as bat COI gene sequences are stored in this repository. See the `sequences` folder.

## Run

1. To reproduce the statistical analyses in our study, pls run the R codes in `R` folder. The script `virus_table_cleaning.R` should be run first.

2. To conduct homology modelling, run `protein_model/homology_modelling/align2d.py` then `protein_model/homology_modelling/model-single.py`.

3. To conduct molecular dynamics analysis, run `1-do_emin_equil.sh`, `2-do_production.sh` and `3-do_analysis.sh` in the `protein_model/MD/modified_scripts` folder sequentially. Please note that our MD simulation pipeline is modified from https://github.com/maxbonomi/bat-MD (Temmam et al., Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells. Nature 604 (2022) 330.).

## Note

For any technical questions, please write to yfpan21 at m.fudan.edu.cn

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