| name | progenomes |
| description | proGenomes4 — nearly 2 million consistently QC'd and annotated high-quality prokaryotic genomes with habitat metadata, pan-genomes, MGE/BGC annotations. Use when: (1) Building large microbial genome reference sets, (2) Comparative genomics / pan-genome analyses, (3) Selecting habitat-filtered genome cohorts, (4) Distinguishing proGenomes from GTDB reps or MGnify biome catalogues. Portal: https://progenomes.embl.de/. For taxonomy releases use gtdb. For biome MAG catalogues use mgnify. For routing use public-databases.
|
| license | MIT |
| category | utilities |
| tags | ["database","proGenomes","genomes","pan-genome","EMBL"] |
| upstream | https://progenomes.embl.de/ |
proGenomes
Portal: https://progenomes.embl.de/
Citation
Fullam, A. et al. proGenomes4: providing 2 million accurately and consistently
annotated high-quality prokaryotic genomes. Nucleic Acids Res. (2025).
https://doi.org/10.1093/nar/gkaf1208
See also docs/references.md.
Analytical thinking
proGenomes is a genome warehouse with uniform QC and multi-workflow
functional annotation (including MGE and BGC calls), habitat metadata, and
precomputed pan-genomes — ~2M genomes / >7B genes / ~33k species in v4.
| Resource | Primary question |
|---|
progenomes | Large consistently annotated prokaryotic genome set |
gtdb | Rank-normalized taxonomy + species clusters / reps |
mgnify | Biome-specific MAG/protein catalogues + analysed studies |
sra-ena | Raw sequencing runs |
Do not assume proGenomes species IDs == GTDB species clusters without mapping.
For MAG novelty in a biome, still use the matching MGnify catalogue + GTDB-Tk.
How to access
https://progenomes.embl.de/
# CLI described in the proGenomes4 paper / site — pin the release you download
Archive: release ID, genome filters (quality, habitat), annotation workflow
names, and download date.
Decision tree
Need many annotated prokaryotic genomes?
├─ Habitat-aware / pan-genome / consistent annotation → progenomes
├─ Taxonomy placement of *my* MAGs → gtdbtk + gtdb
├─ Human-gut (or other biome) species catalogue → mgnify
└─ Benchmark with gold standards → cami
Related skills
public-databases · gtdb · mgnify · gtdbtk · antismash · genomad ·
eggnog-mapper · kegg
