{"id":14066063,"url":"https://github.com/pr2database/pr2database","last_synced_at":"2025-07-29T22:31:03.326Z","repository":{"id":136413776,"uuid":"105268099","full_name":"pr2database/pr2database","owner":"pr2database","description":"Protist Ribosomal Reference database (PR2) - SSU rRNA gene database","archived":false,"fork":false,"pushed_at":"2023-04-19T01:23:52.000Z","size":797303,"stargazers_count":78,"open_issues_count":6,"forks_count":7,"subscribers_count":12,"default_branch":"master","last_synced_at":"2024-08-13T07:11:04.991Z","etag":null,"topics":["18s-rrna","database","eukaryotes","metabarcoding","rrna","taxonomy"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pr2database.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-09-29T12:08:30.000Z","updated_at":"2024-07-18T20:59:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"f4108279-848e-4c0d-99b2-3e2bd3ebf547","html_url":"https://github.com/pr2database/pr2database","commit_stats":null,"previous_names":[],"tags_count":19,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pr2database%2Fpr2database","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pr2database%2Fpr2database/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pr2database%2Fpr2database/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pr2database%2Fpr2database/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pr2database","download_url":"https://codeload.github.com/pr2database/pr2database/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228052695,"owners_count":17862105,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["18s-rrna","database","eukaryotes","metabarcoding","rrna","taxonomy"],"created_at":"2024-08-13T07:04:55.260Z","updated_at":"2025-07-29T22:31:03.313Z","avatar_url":"https://github.com/pr2database.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"\n\u003cimg src=\"https://pr2-database.org/img/pr2_logo_16_9_big.png\" width=\"300\" align=\"right\" /\u003e\n\n# Protist Ribosomal Reference database (PR\u003csup\u003e2\u003c/sup\u003e)\n\n[![Database](https://img.shields.io/badge/database-v.%205.1.0-blue.svg)](https://github.com/pr2database/pr2database/releases)\n![Date](https://img.shields.io/badge/date-02%20Apr%202025-lightgrey.svg)\n![Github\nDownloads(total)](https://img.shields.io/github/downloads/pr2database/pr2database/total.svg)\n\n[Latest news on\nBlueSky](https://bsky.app/profile/pr2-database.bsky.social)\n\n## SSU rRNA gene database\n\nThe [PR\u003csup\u003e2\u003c/sup\u003e database](https://pr2-database.org/) was initiated\nin 2010 in the frame of the BioMarks project from work that had\ndeveloped in the previous ten years in the Plankton Group of the Station\nBiologique of Roscoff. Its aim is to provide a reference database of\ncarefully annotated 18S rRNA sequences using eight unique taxonomic\nfields (from domain to species). At present it contains about 240,000\nsequences. A number of metadata fields are available for many sequences,\nincluding geo-localisation, whether it originates from a culture or a\nnatural sample, host type etc… The annotation of PR2 is performed by\nexperts from each taxonomic groups. One very important project in this\nrespect is [EukRef](https://pr2-database.org/eukref/about/) which has\nrecently decided to merge its effort with PR\u003csup\u003e2\u003c/sup\u003e. EukRef has\nbuilt bioinformatics pipelines that have been used during three\nworkshops dedicated to specific taxonomic groups.\n\nThe web interface now includes links to the sequences of the Ribosomal\nOperon Database (ROD) published in Krabberød, A.K., Stokke, E., Thoen,\nE., Skrede, I. \u0026 Kauserud, H. 2025. [The Ribosomal Operon Database: A\nFull-Length rDNA Operon Database Derived From Genome\nAssemblies](https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.14031).\nMolecular Ecology Resources. 25:e14031.\n\n## Current version\n\n- Version: [5.1.0](https://github.com/pr2database/pr2database/releases)\n\n- Released: 2025-04-02\n\n- DOI:\n  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15129782.svg)](https://doi.org/10.5281/zenodo.15129782)\n\n## Accessing PR2\n\n- [Web interface](https://app.pr2-database.org)\n- [Flat files - latest\n  release](https://github.com/pr2database/pr2database/releases)\n- [R package](https://pr2database.github.io/pr2database/index.html)\n\n## About PR2\n\n- [Documentation](https://pr2-database.org/#documentation)\n- [Statistics](https://pr2database.github.io/pr2database/articles/pr2_01_stats.html)\n\n## Core Team\n\n- [Daniel VAULOT](mailto:vaulot@gmail.com), Station Biologique de\n  Roscoff, CNRS, France and University of Oslo, Norway\n- [Javier del CAMPO](mailto:jdelcampo@ibe.upf-csic.es), Institut de\n  Biologia Evolutiva, Barcelona, Spain\n\n## Scientific committee and contributors\n\n- [PR\u003csup\u003e2\u003c/sup\u003e team](https://pr2-database.org/team/)\n\n## Please cite\n\n- Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L.,\n  Boutte, C. et al. 2013. [The Protist Ribosomal Reference database\n  (PR\u003csup\u003e2\u003c/sup\u003e): a catalog of unicellular eukaryote Small Sub-Unit\n  rRNA sequences with curated\n  taxonomy](http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gks1160).\n  Nucleic Acids Res. 41:D597–604.\n\n## Related Projects\n\n#### 18S rRNA primer database\n\nThe [PR\u003csup\u003e2\u003c/sup\u003e primer database](https://app.pr2-primers.org/) is a\ncompilation of primers found in the litterature with an *in silico*\nanalysis against the PR\u003csup\u003e2\u003c/sup\u003e database.\n\n#### metaPR2\n\nThe [metaPR\u003csup\u003e2\u003c/sup\u003e metabarcode database](https://shiny.metapr2.org)\nis a compilation of metabarcode datasets processed by the dada2 R\npackage and assigned against PR2.\n\n#### Ribosomal Operon Database (ROD) - version 1.2\n\nThe [ROD database](https://github.com/krabberod/ROD) contains\nfull-length eukaryotic ribosomal operons. The database is based on the\ngenome assemblies from NCBI, and the operons are extracted from the\nassemblies. The database currently contains 69,480 operon variants from\nmore than 11,935 genomes.\n\n## Questions ?\n\n- Register to our [element.io discussion\n  board](https://matrix.to/#/#pr2-database:matrix.org)\n\n## Report issues\n\n- Please report any issue on\n  [GitHub](https://github.com/vaulot/pr2_database/issues)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpr2database%2Fpr2database","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpr2database%2Fpr2database","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpr2database%2Fpr2database/lists"}