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CoVSeQ Tools

A collection of tools and scripts to support the analysis and collect metrics on COVID-19 viral data.

Dependencies

These scripts are designed to work in Compute Canada clusters and assume the user is running GenPipes pipelines to analyze their data.

Organization

  • full_reporting: Scripts used to generate the full report covering all runs across all technolgies and sequencing centres
  • illumina_metrics: Scripts used to generate metrics for illumina runs
  • ont_metrics: Scripts used to generate metrics for nanopore runs
  • run_reporting: Scripts used to re-format metrics and create reports for illumina runs