gtdb-taxdump

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question on GTDBr214.1 gtdb taxdump file regarding taxID

6

Hello Thank you for your nice work. I downloaded GTDB taxa to utilize it for kraken database. (the taxonomy files you've created) I utilized GTDBr214.1 taxdump files. I just found...

aababc1

Getting GTDB taxID for newly generated MAGs

6

Hi there, I have MAGs is generated from my own samples and annotated using GTDB-Tk. They have been de-replicated leaving me with a unique set which are not genetically close...

PeterCx

[Question] GTDB plus NCBI kraken2 database building using GTDB grafted NCBI taxonomy

3

Hi Shenwei, We are exploring building a database where we can include bacteria and archaea (from GTDB) and viral database from NCBI, while using NCBI style taxonomy but grafting the...

zztin

Silva database?

14

Hi, Thanks for the gtdb-taxdump. I´m working on Silva , is there any available tax dump ?

davidvilanova

Deleted nodes are kept in merged.dmp

22

I'm trying to parse the GTDB r207 taxdump with [`taxopy`](https://github.com/apcamargo/taxopy) and I got the following error: ```python taxdb = taxopy.TaxDb(taxdb_dir="gtdb-taxdump/R207") ``` ``` KeyError Traceback (most recent call last) /var/folders/h4/7rmy02997p3_xb4qgjzx257c0000gp/T/ipykernel_43701/673983918.py in...

apcamargo