So in qiime, when working with SILVA eukaryotic taxonomy the consensus lineages were not as straight forward as 16S, adding in sub categories.
I think this is a database issue, which I understand they’re trying to solve.
What I want to know is, what would be equivalent to the biom file in qiime (provides otu ID, consensus lineage, sample ID) in qiime2?
The equivalent is a feature table (e.g., FeatureTable[Frequency] artifact being the most frequent type) (which is really just a biom table on the inside). See this tutorial for info on importing biom tables into feature tables, and this forum post on why we now call these “feature tables” instead of older nomenclature (e.g., “otu table” as they were called in qiime1).
However, unlike qiime1, taxonomy information is no longer stored in feature tables. This is stored in a separate artifact as “feature metadata”. This makes things more flexible and transparent (is taxonomy information already appended to my feature table? no! it never is). See here for how to import taxonomy information from outside QIIME2 (in that case, a reference taxonomy file) and here for an example of classifying taxonomy in QIIME2 to product a taxonomy artifact.
This is indeed a database issue that the SILVA folks would handle, but I am not sure whether this is still a problem or not (I don’t work with 18S). My impression was that the qiime compatible files (available here) were filtered to contain specific taxonomic ranks, enabling sensible consensus lineages, but that may just be 16S.
Alright, I had a feeling about the Feature table, thank you!
I contacted SILVA directly and they confirmed that all of the Qiime compatible files for 18S have been filtered similar to the 16S. They also said that the latest version is coming soon (they checked this forum)
Thanks, @megladds, for sharing the info from SILVA! So it sounds like working with the consensus/majority taxonomy files provided in the QIIME-format releases of SILVA should be straightforward for 18S, as it is for 16S.
Very good news that the next release is on its way…