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