Hi @elviscat are you using pyRAD or ipyrad? I have never analyzed Ion Torrent Ampliseq data before, but my understanding is that it is different from RAD-seq-type data in that you develop primers to target across genes with partially overlapping tiled reads. If that is the case then I think some other software might work better. pyRAD and ipyrad assume that your sequenced loci will share a fragmented end and therefore lineup without tiling. I may be wrong though, I don't know all the details of that method. If the data are like RAD-seq then you should be able to assemble the loci in ipyrad, but you may have to tweak some options if read lengths are much longer than Illumina short reads.