The representative genomes available here are non-redundant collections of genomes which include the highest quality genome from every specI species cluster. As many specI clusters could be assigned to a habitat, we also provide habitat specific sets of representative genomes.
| Type | Contigs | Genes | Proteins |
|---|---|---|---|
| Representative genomes | contigs.representatives.fasta.bz2 | genes.representatives.fasta.bz2 | proteins.representatives.fasta.bz2 |
| Aquatic | aquatic.contigs.fa.gz | aquatic.genes.fa.gz | aquatic.proteins.fa.gz |
| Disease associated | disease_associated.contigs.fa.gz | disease_associated.genes.fa.gz | disease_associated.proteins.fa.gz |
| Food associated | food_associated.contigs.fa.gz | food_associated.genes.fa.gz | food_associated.proteins.fa.gz |
| Freshwater | freshwater.contigs.fa.gz | freshwater.genes.fa.gz | freshwater.proteins.fa.gz |
| Host associated | host_associated.contigs.fa.gz | host_associated.genes.fa.gz | host_associated.proteins.fa.gz |
| Host plant associated | host_plant_associated.contigs.fa.gz | host_plant_associated.genes.fa.gz | host_plant_associated.proteins.fa.gz |
| Sediment mud | sediment_mud.contigs.fa.gz | sediment_mud.genes.fa.gz | sediment_mud.proteins.fa.gz |
| Soil | soil.contigs.fa.gz | soil.genes.fa.gz | soil.proteins.fa.gz |
| Type | File |
|---|---|
| Habitats per isolate | proGenomes3_habitat_isolates.tab.bz2 |
| Habitats per specI cluster | proGenomes3_habitat_specI.tab.bz2 |
| Representatives per specI cluster | proGenomes3_representatives_for_each_specI.tsv.gz |
| Marker genes | proGenomes3_markerGenes.tar.gz |
| SpecI clustering data | proGenomes3_specI_clustering.tab.bz2 |
| GTDB taxonomy | proGenomes3_specI_lineageGTDB.tab.bz2 |
| Highly important strains | highly_important_strains.tab.bz2 |
| Excluded genomes | proGenomes3_excluded_genomes.txt.bz2 |
| MGE ORFs | representatives_mge_ORFS.tsv.bz2 |
| MGE annotation | representatives_mge_annotation.tsv.bz2 |
| GECCO biosynthetic gene clusters (GenBank records) | progenomes3_gecco_clusters.gbk.gz |