I’m working with reads from Illumina Miseq.
The length of theoretical amplicon is about 400bp so we perform overlapping PE 2x250 .
I used make.contigs command only with stability file.

mothur > make.contigs(file=stability.files, processors=3)

It worked and I obtained stability.trim.contigs.fasta and I also checked contigs report file, but my worry is that primers and barcode could be probably inside the reads yet,
because I didn’t give to mothur information to trim them. It is true ?

Thanks in advance

It depends on how your sequencing was done. If you used the general approach we outlined in the paper then the primers and indices are already removed. If you sequenced through the primers/barcodes then you’ll need to remove them with trim.seqs.