skDER Representative Genomes for 17 Bacterial Taxa

Genomes belonging to a single genus or order were gathered using a loose search of taxonomic classifications in GTDB R214. By loose we required the string 'g__{GENUSNAME}' to be found in taxonomic info column by GTDB, thus allowing gathering of associated genera (which GTDB suggests are different, but literature/domain experts have yet to rename).

Genomes belonging to a taxa were dereplicated using skDER (v1.0.4) in "greedy" clustering mode with default values for parameters (99% ANI cutoff, 90% AF cutoff).

Overview of Files:

- The 'Genome_Dereplication_Overview.tsv' contains details of all the genomes considered as potential representatives for each taxonomic group and their GTDB R214 taxonomic classifications.

- 17 tar.gz compressed directories are provided. Each compressed directory features representative genomes in FASTA format determined for a particular taxon using skDER with greedy clustering and default cutoffs. Genome assemblies are renamed to feature both the GTDB taxonomic classification and the GCA identifier.
        - Acinetobacter - 1,609 rep genomes (17.4% of 9,221 total genomes considered)
        - Bacillales - 2,958 rep genomes (33.7% of 8,766 total genomes considered)
        - Corynebacterium - 678 rep genomes (40.2% of 1,688 total genomes considered)
        - Cutibacterium - 24 rep genomes (4.8% of 502 total genomes considered)
        - Enterobacter - 852 rep genomes (19.3% of 4,408 total genomes considered)
        - Enterococcus - 923 rep genomes (14.4% of 6,426 total genomes considered)
        - Escherichia - 2,367 rep genomes (6.9% of 34,358 total genomes considered)
        - Klebsiella - 1,001 rep genomes (5.5% of 18,145 total genomes considered)
        - Lactobacillus - 503 rep genomes (28.8% of 1,747 total genomes considered)
        - Listeria - 270 rep genomes (5.3% of 5,062 total genomes considered)
        - Mycobacterium - 723 rep genomes (6.8% of 10,657 total genomes considered)
        - Neisseria - 348 rep genomes (9.7% of 3,235 total genomes considered)
        - Pseudomonas - 2,604 rep genomes (18.5% of 14,066 total genomes considered)
        - Salmonella - 292 rep genomes (2.1% of 14,109 total genomes considered)
        - Staphylococcus - 417 rep genomes (2.1% of 19,627 total genomes considered)
        - Streptococcus - 2,224 rep genomes (12.0% of 18,492 total genomes considered)
        - Streptomyces - 1,539 rep genomes (57.1% of 2,697 total genomes considered)