Welcome to sc-VirusScan’s documentation!

sc-VirusScan is a Snakemake pipeline that enables accurate, sensitive and scalable detection of viral pathogens in single-cell RNA datasets.

The sc-VirusScan integrates the strengths of two standard approaches, a standard mapping based approach and a Kraken2 k-mer based approach which provides rapid taxonomic classification. The output of the sc-VirusScan pipeline can be integrated easily into existing single cell analysis frameworks (Seurat and Scanpy) which can provide standardized and reliable way to scrutinize virus infections at the single cell level resolution.

Contents

• sc-VirusScan Overview
• Installation and Setup
  • Contents of config.yaml file
  • Description of config.yaml file
  • Important Note For Synapse Data Analysis mode
• Pipeline Execution
  • Pipeline Outputs

Credits

sc-VirusScan was developed by Saim Momin as a Master Thesis project for the Bioinformatics Master program of the Saarland University ,under the supervision of Deboutte W and Manke T. at the Bioinformatics Unit of the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.

Help and Support

For feature requests or bug reports, please open an issue on our GitHub Repository.