Hi @koch,
Just to be sure, do you mean the size of the overlap or the final sequence?
Anyway, remember that when you join sequences with DADA2, the denoising happen first and the joining after; thus, your truncate parameters are really important. Thus, the size of the overlap is "given" with the truncate parameters; perhaps this thread will help you if this is your question.
Now, once the sequences are denoised and merged, they become your "representative sequences", thus the final sequence length is the length of your representative.
Hope this helps.