Taxonomic classification 'Taxon' field discrepancies

[SoilRotifer (Mike Robeson)]

Hi @rsak-384,

You can find information about a QIIME 2 formatted prototype of SILVA 138 here:

SILVA 138 Classifiers

This pipeline has been vastly improved via the new RESCRIPt plugin. Which you can check out via the link below. We hope the process of constructing your own reference sequence database (e.g. SILVA) will be far less onerous.

Click here to see the original documentation

I just wanted to let everyone be aware that I've hobbled together a simple <a href="https://github.com/mikerobeson/make_SILVA_db">pipeline</a> for constructing classifiers based …

There will be more information related about this topic soon. So keep your peeled.

To echo, @jwdebelius comments, there are ever ongoing updates with respect to taxonomy. So much so, that there can be substantial conflicts between databases. The online version SILVA db allows you to compare among various taxonomies, like GTDB, etc...

Also, just for a more detailed FYI:

SILVA 138 Classifiers

Hi @prince, To clarify, we do not curate the taxonomy, we are simply parsing the files as provided by SILVA. As for the upper-level taxonomy being propagated downward… this is intended by me. The reason for this is that not all reference sequences have taxonomic annotations for each rank. When a particular rank is missing, in this case the family level, the taxonomic rank above is propagated downward to a lower rank position until it finds a rank at a lower level, then it propagates that rank …

I hope this helps!
-Mike