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jeromekelleher / sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Record spike dropouts for QC #48

Open jeromekelleher opened 1 year ago

jeromekelleher commented 1 year ago

As suggested by @szhan

szhan commented 1 year ago

Amplicon dropouts have been a persistent problem with the ARTIC protocol since version 1. Unsurprisingly, it is still a problem in version 4 (https://www.medrxiv.org/content/10.1101/2022.12.01.22282842v1). Knowledge about where in the genome and in which variants amplicon dropouts frequently happen may help with QC and diagnosing issues in ARG building.