error trim with make.contigs?

I’ve previously used mothur for 454 runs and am undertaking my first miSeq analysis. It seems that the make.contigs command does not allow read trimming for quality, except in the overlap region (using the insert parameter). Since the command doesn’t generate quals files it is not possible to run trim.seqs on the output. This seems like an obvious and necessary thing to do, which probably means that I’m missing how it is intended to be done. In the online miSeq SOP sequencing error is estimated from a mock community but this is not something that we did with this project. Does anyone know what I’m missing? Any help is much appreciated!


I see that there is an extensive discussion of this under feature requests. My two cents is that this would be a great feature to have. The command already takes quality scores into account for overlapped regions, why not trim the non-overlapping regions independently?