DOI: 10.5281/zenodo.11494307
title: GTDB r220 Mash Database (UNOFFICIAL MIRROR)

description: This is an UNOFFICIAL host for the GTDB mash sketch based on GTDB r220

Intended use of this file is to include in the VEBA database for quicker GTDB-Tk analysis. 

Created by running the following command using GTDB-Tk v2.4.0 on the S1 sample from Zenodo:7946802: 

gtdbtk classify_wf --genome_dir veba_output/binning/prokaryotic/S1/output/genomes/  --out_dir test_output -x fa --cpus 1 --mash_db ./gtdb_r220.msh

Source Files: 

gtdbtk_r220_data.tar.gz

RELEASE_NOTES.txt



Release 220.0:
--------------

GTDB release R09-RS220 comprises 596,859 genomes organised into 113,104 species clusters. 
Additional statistics for this release are available on the GTDB Statistics page.

Release notes:
--------------

 - Average nucleotide identity (ANI) between genomes is now calculated using skani (Shaw et al., Nat Methods, 2023) instead of FastANI (Jain et al, Nat Commun, 2018). 
   skani provides a substantial reduction in computational requirements while producing similar ANI values and more accurate alignment fraction (AF) values.
 - CheckM v2 information is included on the website and in the metadata files, noting at this stage that these data were not used for the QC step in release 220. 
 - Post-curation cycle, we identified updated spelling for 15 taxon names: 
    p__Calescibacterota (updated name: Calescibacteriota)
    c__Brachyspirae (updated name: Brachyspiria)
    c__Leptospirae (updated name: Leptospiria)
    o__Ammonifexales (updated name: Ammonificales)
    o__Exiguobacterales (updated name: Exiguobacteriales)
    o__Hydrogenedentiales (updated name: Hydrogenedentales)
    o__Phormidesmiales (updated name: Phormidesmidales)
    f__Arcanobacteraceae (updated name: Arcanibacteraceae)
    f__Acetonemaceae (updated name: Acetonemataceae)
    f__Ethanoligenenaceae (updated name: Ethanoligenentaceae)
    f__Exiguobacteraceae (updated name: Exiguobacteriaceae)
    f__Geitlerinemaceae (updated name: Geitlerinemataceae)
    f__Koribacteraceae (updated name: Korobacteraceae)
    f__Phormidesmiaceae (updated name: Phormidesmidaceae)
    f__Porisulfidaceae (updated name: Poriferisulfidaceae)
   Note that the LPSN linkouts point to the correct updated names. We encourage users to use the updated names as these will appear in the next release.
 - Post-curation cycle, we discovered that two provisionally named families, Nitrincolaceae and Denitrovibrionaceae  have been validly named under the ICNP as Balneatricaceae and Geovibrionaceae, respectively. 
   We encourage users to use the validly published names as these will appear in the next release.
 - We thank Jan Mares for his assistance in curating the class Cyanobacteriia and Brian Kemish for providing IT support to the project.


 

If you have found this useful, please cite the original publications: 



Chaumeil PA, et al. 2022. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database. Bioinformatics, btac672.

Parks, D.H., et al. (2021). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50: D785–D794.