COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow

for paired-end data using the same steps for mapping and variant calling, but

adds extra logic for trimming ARTIC primer sequences off reads with the ivar

package. In addition, this workflow uses ivar also to identify amplicons

affected by ARTIC primer-binding site mutations and excludes reads derived from

such "tainted" amplicons

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