E-Mail: stephan.richter@uni-jena.de
Room: 4007
Phone: +49-3641-9-46007
Publications
2026
Saghaei, Shahram; Siemers, Malte; Ossetek, Kilian L; Richter, Stephan; Edwards, Robert A; Roux, Simon; Zielezinski, Andrzej; Dutilh, Bas E; Marz, Manja; Cassman, Noriko A
VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses Journal Article
In: Nucleic Acids Research, vol. 54, iss. D1, pp. D912–D924, 2026.
@article{nokey_97,
title = {VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses},
author = {Shahram Saghaei and Malte Siemers and Kilian L Ossetek and Stephan Richter and Robert A Edwards and Simon Roux and Andrzej Zielezinski and Bas E Dutilh and Manja Marz and Noriko A Cassman},
doi = {10.1093/nar/gkaf1224},
year = {2026},
date = {2026-01-06},
urldate = {2025-12-17},
journal = {Nucleic Acids Research},
volume = {54},
issue = {D1},
pages = {D912–D924},
abstract = {High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.