metagenmomics in qiime2


I have been googling for a tutorial how to process raw data from shotgun sequencing using qiime2.

If anyone could point me to a tutorial where metagenomics is analyzed from raw data to a matrix where I have sample ids and abundances that would be great.


Welcome to the forum @Carlos_M!

There are two different community-developed plugins to support processing shotgun metagenome data with QIIME 2: q2-metaphlan2 and q2-shogun. You can read more about those, their tutorials, and other QIIME 2 community plugins here:

It is also possible to import shotgun metagenome results from other analysis packages to QIIME 2 as a feature table. The “importing” tutorial on gives details on importing feature tables.

Good luck!


Hi @Nicholas_Bokulich,

I took a look at the metaphlan2 tutorial and the graphic that they show in the overview here suggests that I get relative abundances as output. Do you know if I also have the option to get the absolute count? E.g. for some statistical analyses I would like to use clr transformed count values as these analyses do not make sense with relative abundances. So best would be to get the absolute counts with the readcounts.

Do you know that?

@fasnicar may be able to provide details on (q2-)metaphlan2

In MetaPhlan you can use the -t clade_profiles to get a normalized marker counts for each clade that has a non-null marker, but with MetaPhlAn you won’t be able to get absolute count, because only reads that map to a marker can be considered.