Hi Luca,
Many thanks for the suggestion, I've tried and the reads are shorter but not quite there yet!
This is m first go with 454 sequences, so I am not sure if this is normal. I think I am looking at something similar to this one, as suggested there, I'll try RESCRIPt, I'm just unsure about --i-reference-sequences reference-sequences.qza , can this be any other sequences, i.e. not 454 but Illumina?