A pipeline for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.

To run VIPERA locally with the default configuration, you only need one line of code after installing Snakemake, configuring the inputs and outputs and the context dataset:

snakemake --use-conda -c4  # runs VIPERA on 4 cores (reccomended)

Alternatively, you can use a simple script that downloads the data from our study and performs the analysis in one step:

./run_default_VIPERA.sh

This Snakemake workflow can be also executed in an HPC environment.

Please refer to config/README.md for detailed setup instructions.

Álvarez-Herrera M. & Sevilla, J., Ruiz-Rodriguez, P., Vergara, A., Vila, J., Cano-Jiménez, P., González-Candelas, F., Comas, I., & Coscolla, M. (2023). VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. bioRxiv. https://doi.org/10.1101/2023.10.24.561010

@misc{AHS_VIPERA_2023,
  title = {{VIPERA}: {Viral} {Intra}-{Patient} {Evolution} {Reporting} and {Analysis}},
  shorttitle = {{VIPERA}},
  author = {Álvarez-Herrera$^*$, Miguel and Sevilla$^*$, Jordi and Ruiz-Rodriguez, Paula and Vergara, Andrea and Vila, Jordi and Cano-Jiménez, Pablo and González-Candelas, Fernando and Comas, Iñaki and Coscolla, Mireia},
  url = {https://www.biorxiv.org/content/10.1101/2023.10.24.561010},
  doi = {10.1101/2023.10.24.561010},
  language = {en},
  urldate = {2023-10-25},
  publisher = {bioRxiv},
  note = {$^*$ indicates equal contribution}
}