The annotation script should read the BED file (or similar) and use the MiniMap2 coordinates to infer the amplicon for each read. Some QC could also be done here - I.e. filter multi amplicon chimeras etc. The amplicon number would be added as a column in the annotation CSV file for use by the RAMPART UI.
The annotation script should read the BED file (or similar) and use the MiniMap2 coordinates to infer the amplicon for each read. Some QC could also be done here - I.e. filter multi amplicon chimeras etc. The amplicon number would be added as a column in the annotation CSV file for use by the RAMPART UI.