SARS-CoV-2

[lskatz]

Is your feature request related to a problem? Please describe.
We need to run SARS-CoV-2 through SneakerNet

Describe the solution you'd like

A new workflow with new plugins

• Amplicon-based read metrics
• SARS-CoV-2 genome assembly
• Gene prediction and annotation (vadr)
• Pass/fail
  • coverage (proposed: 10x)
  • breadth of genome

Describe alternatives you've considered
QCing outside of SN?

Additional context
Point of contact: PulseNet NGS Laboratory

• Might also need a method for splitting a mixed run of SARS-CoV-2 from other genomes

[lskatz]

More pass/fail:

• Coverage might be more like 100x but 20-30x is probably sufficient
• 99% of the breadth of the genome assembly
• Look for all CDS recovered