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proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A,
Letunic I,
Schmidt TSB, Ducarmon QR, Karcher N,
Khedkar S,
Kuhn M, Larralde M,
Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C,
Schudoma C,
Szklarczyk D,
Sunagawa S,
Zeller G,
Huerta-Cepas J,
von Mering C,
Bork P,
Mende DR Abstract + PDF
The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.