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.
We are collecting user feedback on which genomes should be considered as representatives. Search and select your favourite genome below to add your vote.
| 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 |
| Type | File |
|---|---|
| Functional annotations for representative genomes | proGenomes4_rep_eggnog.tsv.gz |