Pipelines for SARS-CoV-2 subgenome project

This repository includes all the codes and analysis pipelines for studying the SARS-CoV-2 subgenome landscape.

• workflow: Analysis pipeline in Snakemake language.

  • mapping: Mapping of NGS and Nanopore data
  • pairing: Analyzing template switch events and RNA-RNA interaction modes
  • subgenome: Analzying subgenome landscape

  The Python/R scripts are included in the subdirectories of workflow.

Authors

• Dehe Wang
• Xinghai Yu
• Yu Zhou