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SARS-CoV-2 #53

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lskatz opened this issue Oct 27, 2020 · 1 comment

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lskatz commented Oct 27, 2020

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 added the enhancement label

Owner Author

lskatz commented Oct 27, 2020

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

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