viral-ngs: genomic analysis pipelines for viral sequencing

Contents

• 1. Description of the methods
• 2. Command line tools
  • 2.1. reports.py - produce various metrics and reports
  • 2.2. illumina.py - for raw Illumina outputs
  • 2.3. broad_utils.py - for data generated at the Broad Institute
  • 2.4. file_utils.py - utilities to perform various file manipulations