40 A crash course in SARS-CoV-2 bioinformatics
Jan 18, 2021•57 min
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Episode description
Over the last year we've learnt a lot about SARS-CoV-2 genomics. Lee extracts all the insider knowledge from our brains and we give him the honest truth to his probing questions.
We cover:
Pipelines for SARS-CoV-2
Archives & metadata
Read filtering
Assembly vs consensus
Amplicon data analysis
Controls
If things look too good
Coverage
....
Some URLs:
https://github.com/connor-lab/ncov2019-artic-nf
https://github.com/jts/ncov-tools
https://github.com/lskatz/SARS-CoV-2-trueTree
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