This is something I have never seen, so I would like you all to ask a question. What could have gone wrong (probably with sequencing) so that I have received this quality data? Screenshots below shows overall and a little bit zoomed-in demux.qzv. I don’t think that it is possible to do a healthy analysis.
Sequencing platform is miseq if it would be any help. 250x8x8x250 cycles. The work is V4.