GTDB r226 Mash Database (UNOFFICIAL MIRROR)

This is an UNOFFICIAL host for the GTDB mash sketch based on GTDB r226 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 v2.4.1 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_r226.msh Source Files: gtdbtk_r226_data.tar.gz RELEASE_NOTES.txt Release 226.0: -------------- GTDB release R10-RS226 comprises 732,475 genomes organised into 143,614 species clusters. Additional statistics for this release are available on the GTDB Statistics page. Release notes: -------------- - Post-curation cycle, we identified updated spelling for 1 taxon and a valid name for a placeholder: g__Prometheoarchaeum (updated name: Promethearchaeum) f__MK-D1 (updated name: Promethearchaeaceae) 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. - QC criteria for GTDB was modified to consider CheckM v1 and v2 completeness and contamination estimates. In order to pass QC, a genome must have completeness >=50%, contamination <5%, and quality (completeness - 5*contamination) >=50% using both the CheckM v1 and v2 estimates. The exception is that a contig comprised of <10 contigs passes QC if these criteria are meet be either CheckM v1 or v2. - Mash is no longer used as a prefilter for establishing GTDB species clusters as this was found to be unnecessary with the prefiltering provided internally by skani (Shaw et al., Nat Methods, 2023). - The 20% most heterogeneous sites were removed from the archaeal MSA using alignment_pruner.pl (https://github.com/novigit/broCode/blob/master/alignment_pruner.pl). - The GTDB taxonomy tree now provides links to Sandpiper (https://sandpiper.qut.edu.au) results which provide information about the geographic and environmental distribution of a taxon. - We thank Jan Mares for his assistance in curating the class Cyanobacteriia, Peter Golyshin for bringing Ferroplasma acidiphilum strain Y (GCF_002078355.1) to our attention, 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.