Latest GTDB topics - GTDB Forum

Topic	Replies	Views	Activity
FAQ / Guidelines How can I classify my own genomes with the GTDB? We have developed a stand-alone application called GTDB-Tk. A specific FAQ for GTDB-Tk can be found here What is the GTDB versioning scheme? The GTDB version indicates b…	1	2521	August 5, 2020
About the GTDB category	0	899	August 5, 2020
Possible to provide a test database	3	19	January 9, 2025
Contamination in Pseudomonas sp000955805	2	24	October 11, 2024
Inquiry Regarding Matching 16S rRNA genes and MAGs	1	362	November 14, 2024
Determining uncultured bacterial group/clade from GTDB data	2	20	November 12, 2024
MAG or Isolate and ambiguous checkm scores	1	20	October 30, 2024
Release220 - wrong md5hashes	2	28	October 27, 2024
Phylogenetic tree bootstrap values	2	18	September 6, 2024
Bac120_r207.tree missed some taxa	0	16	August 28, 2024
Pplacer requirements	5	2090	July 16, 2024
Marker gene phylogeny vs ANI and AF	2	119	June 12, 2024
Is there a difference in GTDB-taxonomy and metadata between Genbank and Refseq genomes of the same assembly?	1	177	May 29, 2024
Should samples be separated by tissue type during GTDB assignment?	0	124	May 3, 2024
R phyloseq and GTDB	0	150	April 19, 2024
Obtaining taxonomic ranks for genome accession numbers	1	183	March 28, 2024
Discrepancy between "type_species_of_genus" online and metadata file	1	219	March 28, 2024
Can we know if GTDB Sequences uses Poly(A) tails?	3	204	March 6, 2024
Note: the number of downloadable GTDB complete genomes mismatched with that in official website due to some records are deleted in NCBI	2	248	February 20, 2024
GTDB taxonomy of bv-brc (formerly Patric) genomes	2	450	February 14, 2024
Scoring representative genomes	2	213	February 6, 2024
Retrieve the number of species represented by a single genome	2	236	February 6, 2024
Is GTDB including all species from NCBI bacteria refseq?	1	282	January 24, 2024
Missing genera in NCBI / GTDB mapping files	1	268	January 8, 2024
How to obtain reference genome sequences in GTDB database	6	852	December 14, 2023
Growth temperature metadata for GTDB	0	308	December 1, 2023
Genomes download	1	454	November 22, 2023
The ANI between species within a same genus is notably low	2	500	October 27, 2023
Downloading the genomes of all Staphylococcus saprophyticus available in GTDB	2	617	October 15, 2023
MD5SUM.txt not matching filenames on latest	0	483	July 3, 2023

FAQ / Guidelines

How can I classify my own genomes with the GTDB? We have developed a stand-alone application called GTDB-Tk. A specific FAQ for GTDB-Tk can be found here What is the GTDB versioning scheme? The GTDB version indicates b…