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

We provide a simple script that downloads the data from our study and performs the analysis in a single step:

./run_default_VIPERA.sh

This Snakemake workflow is compatible with both local execution and HPC environments utilizing SLURM. It supports dependency management through either conda or Singularity, as detailed in the run modes documentation.

Please refer to the full workflow documentation for detailed setup instructions.

The documentation in this repository provides instructions for running VIPERA with Snakemake <8. We recommend using Snakemake 7.32. However, using Snakemake 8 is possible with minimal modifications (see the migration documentation). For example, --use-conda and --use-singularity are deprecated in Snakemake 8, and --software-deployment-method conda apptainer is the preferred way to provide the options. Additionally, SLURM support is only available after installing an executor plugin for slurm.

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}
}