If your data has already had the barcode and primer sequences removed, is it still necessary to run the trim.seqs command when pre-processing the data? If you don’t have an oligos file and a qual file, will the trim.seqs command still work to remove other erroneous sequences?
It will remove sequences that are short, long, have ambiguous bases, or long homopolymers. These can all be done with screen.seqs as well. trim.seqs can also chop sequences to remove the last N bases or keep the first N bases.