diversity and taxonomy analysis with combined feature table and taxonomy.biom file

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You may have noticed that QIIME 2 differs from QIIME 1 in some respects. One of these differences is that the feature-table (i.e. OTU-table) is kept separate from the taxonomy data. That is, there is no single file that will contain both the OTUs / ASVs and the taxonomy. This has to do with the type system, and to keep things modular. If you look through the "Moving Pictures" tutorial, you'll see that some commands require both a feature and taxonomy data as inputs. For example, to make a barplot you have to provide these two files:

qiime taxa barplot \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization taxa-bar-plots.qzv

You'll have to export your biom data as a TSV file you'll find many examples of how to do so with the biom convert command. For example:

biom convert -i table.biom -o table.from_biom.txt --to-tsv

You can look through the forum to see how others have imported these and other file types. For example, here is how to import a taxonomy.tsv file.

You can also import both parts of the biom table (OTUs and Taxonomy) like this.

-Cheers!

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