Is it bad to manually adjust taxonomy to clean up names and fix some of the taxonomic levels? For some of my sequences, the classified genus does not align with the classified genus. I used the latest version of SILVA for classification.
For example, a sequence variant that at the genus level is classified as Synechococcus, is classified as Pseudanabaenales at the order level…
In addition to this I have some where a classified genus is Aphanizomenon but then at the species level it is listed as Anabeana sp. A bit confusing since these are two different genus (although from the same order at least!)
Okay, the wonderful and brilliant @Mehrbod_Estaki has suggested that i may have mis-read yoru question. (If so, I apologize to all involved). I don’t think it’s a good idea to manually update specific taxonomy in a database unless you’re describing it as ‘manually curated’. (And then you realease said manual curation.) The database may be wrong, but it’s going to be wrong in the same way for everyone, which at least leads to reproducible wrongness.
I would also double check the GTDB, because they have made big taxonomic shifts which may not be reflected other places. I think t here’s an online browswer.