Use of option template or reference in classify.seqs?


In the MiSeq SOP classify.seqs is used with the option “reference” for the reference taxonomy fasta whereas in the 454 SOP and the classify.seqs documentation “template” is used. Can they be used interchangeably? What is the difference?
I tried browsing the underlying source code (classifyseqscommand.cpp and it’s header file) on github but sadly c++ is not my strong suit :frowning: .

Kind regards,


They can be used interchangeably. We changed the parameter name, but allowed both names to make mothur more user friendly for our longtime mothur fans.

Ok, thanks for the clear & swift reply :smiley: