SARS-CoV-2 - Githubissues

lskatz / SneakerNet

:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run

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SARS-CoV-2 #53

Open lskatz opened 3 years ago

lskatz commented 3 years ago

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 commented 3 years ago

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