Mycobiome tools

Hi friends! I want to open an offtopic. I have some skills about 16S rDNA amplicon approach for Microbiome analysis using QIIME2, but I’m completely neofyte in the Mycobiome world. Now, I’m interested in perfoming an analysis of the fungal community from a set of faecal samples. Could anyone explain me how to perform such kind of analysis? I mean, pipelines, bioinformatic tools, etcetera. My starting point are ITS amplicon reads sequenced in a Miseq platform.
I wish it would exist something as wonderful as QIIME2 for fungi analysis!
Thanks a lot

QIIME 2 is NOT 16S-specific, and indeed folks are using it for analysis of fungi, other microbial eukaryotes, and non-microbial eukaryotes (e.g., with COI). Just peruse this forum to see how folks are using QIIME 2 to examine all domains of life. There are even tutorials! E.g.,


I was not aware of that functions of QIIME2!
Thanks a lot for the links and for the quick answer :wink: