The "amplicon type" is basically a description of a PCR amplicon, and which part of said amplicon is actually sequenced.
+This information is important because given primers will be removed from the reads during the analysis.
In the ViroConstrictor pipeline the primer-removal is done by our tool AmpliGone.
+The information regarding the "amplicon type" is required because it tells te pipeline, and therefore also AmpliGone, from which side(s) of a read the primer-sequence has to be removed.
+Currently there are two options: "End-to-End" or "End-to-Mid".
+In short: "End-to-End" means that the sequenced read covers the full length of an amplicon. Meaning that the primer-sequence is present at both ends of a read.
+"End-to-Mid" means that the sequences read only partially covers the length of the amplicon. Meaning that the primer-sequence is present at only one end of a read.
Also see the AmpliGone documentation regarding amplicon-types where we go into more detail regarding these types and what these terms mean.
+Please check your sequencing and laboratory setup for the amplicon type to match your analysis to ensure the best results.