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PreprintCC BY-NC-NDbioRxiv

GenomeCompendium: A database for the integrated analysis of repeats, assembly quality and functional content of complete prokaryotic genomes

  • T. Totu
  • G. Jaques
  • B. Heiniger
  • T. Segessemann
  • M. Schmid
  • M. Bourqui
  • A. Wicki
  • J. E. Frey
  • C. H. Ahrens1
  1. 1Agroscope
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Abstract

Microorganisms hold great promise for urgent global needs such as increasing sustainable agricultural production while reducing chemical fertilizer and pesticide use or providing novel classes of antimicrobials/therapeutics. Moving from analyzing microbiome composition to applying synthetic communities and studying their functions requires access to isolates and complete genome sequences. By spanning the frequent repeats, long-read sequencing can resolve complex prokaryotic genomes, yet error-prone short-read assemblies dominate. We here release the GenomeCompendium, a public database and interactive analysis tool for complete prokaryotic genomes (https://genome-compendium.com/). Using NCBI RefSeq (~47,000) and GenBank (~13,000) genomes, we integrated available metadata, GTDB taxonomy and computed features including repeat classes and gene content screening, intragenomic 16S rRNA sequence identity, and biosynthetic gene cluster co-occurrences. Evaluating repeat content and assembly complexity metrics, we identify taxonomic ranks dominated by difficult-to-assemble genomes and show that complex, repeat-rich genomes are more common than previously estimated. By mining metadata, our quality control flags 6.3% of RefSeq assemblies as potentially erroneous or incomplete. As valuable reference for data mining and to track taxonomic coverage, the GenomeCompendium links ~90 features across genomes, offers downloadable reports and -as unique features- pre-computed proteogenomics databases to improve genome annotations of RefSeq strains and the ability to analyze any uploaded prokaryotic genome.

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Cite

BibTeXRIS
BibTeX
@misc{totu2026genomecompendium,
  title = {{GenomeCompendium: A database for the integrated analysis of repeats, assembly quality and functional content of complete prokaryotic genomes}},
  author = {T. Totu and G. Jaques and B. Heiniger and T. Segessemann and M. Schmid and M. Bourqui and A. Wicki and J. E. Frey and C. H. Ahrens},
  howpublished = {bioRxiv},
  year = {2026},
  month = aug,
  doi = {10.64898/2026.08.14.744864},
  url = {https://www.biorxiv.org/content/10.64898/2026.08.14.744864v2},
  note = {CC BY-NC-ND},
}
RIS
TY  - UNPB
TI  - GenomeCompendium: A database for the integrated analysis of repeats, assembly quality and functional content of complete prokaryotic genomes
AU  - T. Totu
AU  - G. Jaques
AU  - B. Heiniger
AU  - T. Segessemann
AU  - M. Schmid
AU  - M. Bourqui
AU  - A. Wicki
AU  - J. E. Frey
AU  - C. H. Ahrens
PY  - 2026
DA  - 2026/08/14
PB  - bioRxiv
DO  - 10.64898/2026.08.14.744864
UR  - https://www.biorxiv.org/content/10.64898/2026.08.14.744864v2
AB  - Microorganisms hold great promise for urgent global needs such as increasing sustainable agricultural production while reducing chemical fertilizer and pesticide use or providing novel classes of antimicrobials/therapeutics. Moving from analyzing microbiome composition to applying synthetic communities and studying their functions requires access to isolates and complete genome sequences. By spanning the frequent repeats, long-read sequencing can resolve complex prokaryotic genomes, yet error-prone short-read assemblies dominate. We here release the GenomeCompendium, a public database and interactive analysis tool for complete prokaryotic genomes (https://genome-compendium.com/). Using NCBI RefSeq (~47,000) and GenBank (~13,000) genomes, we integrated available metadata, GTDB taxonomy and computed features including repeat classes and gene content screening, intragenomic 16S rRNA sequence identity, and biosynthetic gene cluster co-occurrences. Evaluating repeat content and assembly complexity metrics, we identify taxonomic ranks dominated by difficult-to-assemble genomes and show that complex, repeat-rich genomes are more common than previously estimated. By mining metadata, our quality control flags 6.3% of RefSeq assemblies as potentially erroneous or incomplete. As valuable reference for data mining and to track taxonomic coverage, the GenomeCompendium links ~90 features across genomes, offers downloadable reports and -as unique features- pre-computed proteogenomics databases to improve genome annotations of RefSeq strains and the ability to analyze any uploaded prokaryotic genome.
ER  -