Mycobiome tools

[Nicholas_Bokulich]

@Manuss_Ponce

I wish it would exist something as wonderful as QIIME2 for fungi analysis!

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.,

Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences

Yes, I added support for the output of unmerged reads last month. Update itsxpress and q2-itsxpress and you should be all set. The itsxpress tutorial has also been updated with instructions on outputting unmerged reads for Dada2.

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QII…