mothur

Using MED (minimum entropy decomposition)

Hi

I am using 16s data generated from the Miseq illumina SOP and I would like to try MED (http://merenlab.org/2014/11/04/med/#the-manuscript) on the quality filtered-sequences (not the unique sequences). Which of the files is most appropriate to use, this one: stability.trim.contigs good fasta (around 3 GB for my data). ?

Thank you!

Kristin