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proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes

The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this chall...

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Main Authors: Fullam, Anthony (Author) , Letunic, Ivica (Author) , Maistrenko, Oleksandr M. (Author) , Castro, Alexandre Areias (Author) , Coelho, Luis Pedro (Author) , Grekova, Anastasiia (Author) , Schudoma, Christian (Author) , Khedkar, Supriya (Author) , Robbani, Mahdi (Author) , Kuhn, Michael (Author) , Schmidt, Thomas S. B. (Author) , Bork, Peer (Author) , Mende, Daniel R. (Author)
Format: Article (Journal)
Language:English
Published: 6 January 2026
In: Nucleic acids research
Year: 2026, Volume: 54, Issue: D1, Pages: D852-D857
ISSN:1362-4962
DOI:10.1093/nar/gkaf1208
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1093/nar/gkaf1208
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Author Notes:Anthony Fullam, Ivica Letunic, Oleksandr M. Maistrenko, Alexandre Areias Castro, Luis Pedro Coelho, Anastasiia Grekova, Christian Schudoma, Supriya Khedkar, Mahdi Robbani, Michael Kuhn, Thomas S. B. Schmidt, Peer Bork, Daniel R. Mende
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Summary:The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/.
Item Description:Veröffentlicht: 20 November 2025
Gesehen am 06.03.2026
Physical Description:Online Resource
ISSN:1362-4962
DOI:10.1093/nar/gkaf1208

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