I'm new to NGS and am submitting amplicons of similar sequences out for illumina. I initially just want to quantify the relative representation of these sequences.

The library for sequencing looks like.

5’ sequencing primer – forward primer – sequence of interest – reverse complement of reverse primer – reverse complement of 3’ sequencing primer

I am wondering if this workflow makes sense:

1. Trim Illumina adapters and the primers from both ends.
2. Merge reads.
3. Throw away anything that is too similar to disentangle (some threshold on length)

I believe the similarity of the sequencing poses an issue for merging.