All sequences treated as unique with get.groups

Ridiculous question that proves I’m struggling to understand all of the steps:
Should the output of get.groups be aligned? Or rather, does it matter one way or the other?

I am using Oxford Nanopore data on full length 16S, so I am expecting a silly high error rate and all manner of other problems, I just want to see what is possible with this data set. When I run get.groups prior to assessing my error rate, Mothur is treating all 992 of my mock community sequences as unique. Is this likely just a side effect of having too much error? Or, does it suggest that I have gone awry at a previous step?

I’m assuming that it’s the former, but I want to make sure the gaps in the sequences are not part of the issue, and/or there’s not something else I am missing.

If you give it an alignment file then the outputted fasta file should be aligned. This is basically how we use it in the MiSeq SOP


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