Hi, we sequenced 16S rRNA amplicons with illumina. After removing the primer sequence and duplicates, the reads are mostly 60 nt long and all reads start exactly at the same position on the 16S gene, i.e., the sequences are already aligned by default. Is there any point in running align.seqs or can I skip this step and generate OTUs and clusters?
Thank you,


Yeah, I’d still run align.seqs since the ones that aren’t aligned will go wonky. Also, 16S genes have a lot of insertions/deletions that you’ll want to account for with the aligner.