The representative genomes available here are non-redundant collections of genomes which include the highest quality genome from every ANI species cluster. As many ANI clusters could be assigned to a habitat, we also provide habitat specific sets of repre sentative genomes.
| Type | Contigs | Genes | Proteins |
|---|---|---|---|
| Representative genomes | pg4_genomes_representatives.fna.gz | pg4_genes_representatives.fna.gz | pg4_proteins_representatives.faa.gz |
| Aquatic freshwater | aquatic_freshwater.genomes.fa.gz | aquatic_freshwater.genes.fa.gz | aquatic_freshwater.proteins.fa.gz |
| Aquatic | aquatic.genomes.fa.gz | aquatic.genes.fa.gz | aquatic.proteins.fa.gz |
| Aquatic sediment mud | aquatic_sediment_mud.genomes.fa.gz | aquatic_sediment_mud.genes.fa.gz | aquatic_sediment_mud.proteins.fa.gz |
| Disease associated | disease_associated.genomes.fa.gz | disease_associated.genes.fa.gz | disease_associated.proteins.fa.gz |
| Food associated | food_associated.genomes.fa.gz | food_associated.genes.fa.gz | food_associated.proteins.fa.gz |
| Host associated | host_associated.genomes.fa.gz | host_associated.genes.fa.gz | host_associated.proteins.fa.gz |
| Host plant associated | host_plant_associated.genomes.fa.gz | host_plant_associated.genes.fa.gz | host_plant_associated.proteins.fa.gz |
| Soil | soil.genomes.fa.gz | soil.genes.fa.gz | soil.proteins.fa.gz |
| Type | File |
|---|---|
| Highly important strains | pg4_highly_important_strains.tsv.gz |
| Excluded genomes | pg4_excluded_genomes.txt.gz |
| ANI representatives | pg4_representatives_for_each_ANI_cluster.tsv.gz |
| ANI clustering | pg4_ANI_clustering.tsv.gz |
| Functional annotations for representative genomes | pg4_eggnog_representatives.tsv.gz |
| Consensus taxonomy per ANI cluster | pg4_consensus_gtdb_taxonomy_per_ani_cluster.tsv.gz |
| GTDb to NCBI taxonomy mapping | pg4_ncbi_taxonomy.tsv.gz |