DRGM: metadata, genomes, proteins, rgi

This record contains the metadata tables, genome sequences, protein catalogs, and antibiotic resistance gene predictions of DRGM. Species pangenomes and the Kraken2/Bracken databases built from this catalog are deposited as separate records. Metadata DRGM_genome_metadata.tsv : per-genome information for all 33,893 MAGs - genome name, species cluster, representative flag, source dataset and sample, continent and country, CheckM2 completeness and contamination, GUNC pass, length, N50, 5S/16S/23S rRNA and tRNA counts, quality tier, CDS count, and GTDB R220 taxonomy (full classification plus domain to species) DRGM_cluster_metadata.tsv : cluster-level information for the 931 species - representative genome, number of member genomes, how many are medium-quality and near-complete, whether the cluster is medium-quality only, and GTDB R220 taxonomy Representative genomes DRGM_representative_genomes.tar.gz : genome sequences (FASTA) for the 931 DRGM representative genomes, one per species All genomes DRGM_all_genomes.tar.gz : genome sequences (FASTA) for all 33,893 metagenome-assembled genomes used to define the DRGM species, grouped by the species cluster they belong to Proteins Protein catalogs at six levels of redundancy. "unique" holds the sequences left after exact-duplicate removal; the others are clustered at the stated amino-acid identity. Clustering at 100% identity is therefore not the same as the unique set, since the sequences in a family need not be of equal length. DRGM_unique_proteins.tar.gz : unique protein sequences after redundancy removal DRGM_100_proteins.tar.gz : protein families at 100% identity DRGM_95_proteins.tar.gz : protein families at 95% identity DRGM_90_proteins.tar.gz : protein families at 90% identity, with functional annotation DRGM_70_proteins.tar.gz : protein families at 70% identity DRGM_50_proteins.tar.gz : protein families at 50% identity Each archive contains, with {level} being unique, 100, 95, 90, 70 or 50: DRGM_{level}_proteins.rep_seq.faa : representative amino-acid sequence of each family DRGM_{level}_proteins.cluster_info.tsv : family membership at this level DRGM_{level}_proteins.cluster_info_cumulative.tsv : family membership traced back to the individual proteins The 90% archive additionally contains the functional annotation: DRGM_90_proteins.emapper.annotations, .emapper.hits, .emapper.seed_orthologs : eggNOG-mapper output DRGM_90_proteins.deepgoplus.filtered.tsv, .deepgoplus.unfiltered.tsv : DeepGOPlus predictions output Sequence and table files are stored uncompressed inside the archives. Antibiotic resistance genes DRGM_rgi.tar.gz : RGI results against CARD for all 931 species, one directory per species