16S_V6 Ion Torrent data

Dear all,

we recently started a 16S rRNA (V6) project for oral micorbiomes.
We generated a amplicon library which we sequenced by the Ion Torrent PGM.
Is there any workflow/ guide for the analysis of Ion Torrent sequencing files (sff, fastq)
in mothur???

Thanks for the help.

Kind regards,

we’re on it - but beware that the PGM data quality is reallllly bad.