Good morning @colinbrislawn !
Are you working with this kit too, or a similar kit from a different manufacture?
Yes, we have used it once. The situation we had to deal with was exactly the same than the one described in the post you have pasted. Thank you!
do they truly look random, or do you see a bimodal distribution with peaks around the V3 and V4 lengths?
As Thermofisher sent us only the V3 and V4 amplicons the read length distribution looks like bimodal so , as you mentioned, it was easy to split them by length. I was thinking about a more complex situation, in which you have all the amplicons in the same fastq.
It might be useful to have a plug-in to deal with this situation, specially for people that has little experience with microbiomes. In any case, this post provides a wide range of possible solutions.
Thank you very much for the discussion!