Importing Qiime2 biom file with taxonomy to phyloseq

[jairideout (Jai Ram Rideout)]

Hi @colinbrislawn!

@colinbrislawn

I really liked that Qiime 1 would include taxonomy by default, and I would also like to know the best way to handle this going forward with Qiime 2.

In QIIME 2, we decided to store feature tables separately from taxonomy annotations for a few reasons, see @gregcaporaso's summary here:

Feature-table filter-samples removes taxonomy from biom table

We had some discussion offline and in a recent developer call about including taxonomy in .biom files in QIIME 2, but have decided that that is not something we’ll support. Here’s the justification I gave @antgonza about this (there is some overlap with other content in this topic so just noting that the following wasn’t originally written as a reply to this post, but we decided it might help to share this here): @antgonza, following up on your question about supporting taxonomy in biom files …

This design decision makes things a little harder to interoperate with other software expecting a .biom file containing taxonomy annotations, but keeping the two pieces of data separate buys users and developers a lot when operating within QIIME 2. This was a tough decision; there are definitely pros and cons to either approach! Luckily it is easy to export your data and combine the two files, so there is always an "escape hatch" for users.

In general, when you're working in QIIME 2 you'll have two separate .qza files: one is the FeatureTable artifact, and the other is the FeatureData[Taxonomy] artifact. If you want to export these data for use with external programs, you can use qiime tools export to export a .biom file and TSV taxonomy file. You can then use biom add-metadata to add the taxonomy annotations to the .biom file (see this forum topic for examples).

Note: in @gregcaporaso's summary I linked to above, he describes how to import a .biom file containing taxonomy annotations into a FeatureData[Taxonomy] artifact. Thus, it is relatively straightforward to import a .biom file containing taxonomy annotations into QIIME 2 -- just run two import commands on the same .biom file (one command will specify --type FeatureTable[Frequency], the other will use --type FeatureData[Taxonomy]).