weird taxanomic annotations

[SoilRotifer (Mike Robeson)]

Hi @Yin_Hui_Cheok,

If you search the forum you'll find that these questions have been addressed before. For #1 see:

SILVA taxonomy - strange genus names

Welcome to the forum, @GreenDragon! Unfortunately, these annotations are so vague that it is really unclear what they could represent and if they are theoretically same or separate entities. Given that you are receiving these classifications for distinct ASVs is a pretty good indication that they do represent distinct taxa, but you could look at those ASVs to decide for yourself whether it is worth collapsing. If I were in your shoes, I would keep separate. Though for your purposes maybe it m…

and

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 …

For # 2 see:

SILVA taxonomy naming conventions

Hi everyone, Does anyone know why taxonomy in SILVA sometimes have square brackets? Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Anaerotruncus;[Clostridium]_leptum Why not just Clostridium leptum instead of [Clostridium] leptum? Does this have any significance, or is it just an error? Secondly, it is my understanding that some taxa which lack formal classification are placed in groups (eg. Bacteroidales_S24_7_group). Does “S24_7” convey any information? What the naming conven…

-Mike