Hi @natavicula,
I'm currently messing around with decontam based on this introduction:
https://benjjneb.github.io/decontam/vignettes/decontam_intro.html#identifying-contaminants-in-marker-gene-and-metagenomics-data
I also used the prevalence method which detected a few contaminate sequences in my batches, but my question is how did you go forward after identifying the contaminates? The intro just kind of stop after the identification and I can't seem to find the best way to remove them (unless the idea is I just need to delete the rep-seqs that are contaminations). What did you do to remove your contamination after decontam identified them?
Thanks,
Zach