Hi Pat, Sarah: I work with 60-bp Illumina reads from 16S amplicons. When I use screen.seqs, I’m always in doubt how stringent the parameters need to be set such that I remove the junk, w/o removing too many genuine sequences. For instance I wonder if criteria=90 might be too stringent for my dataset. When I look at the align report, I see quite a range of similarity values and I thought it could be useful to have the option in screen.seqs to remove sequences which fall below a certain similarity threshold, say, 70% (similarity=XX). I suspect someone may already have made a similar request, but I don’t see it under feature requests. Unfortunately the search feature in forum doesn’t seem to work, so I may have overlooked related suggestions.
thanks for your good work,