Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/pr2database/pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
https://github.com/pr2database/pr2database
18s-rrna database eukaryotes metabarcoding rrna taxonomy
Last synced: 3 months ago
JSON representation
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
- Host: GitHub
- URL: https://github.com/pr2database/pr2database
- Owner: pr2database
- License: mit
- Created: 2017-09-29T12:08:30.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2023-04-19T01:23:52.000Z (almost 2 years ago)
- Last Synced: 2024-08-13T07:11:04.991Z (6 months ago)
- Topics: 18s-rrna, database, eukaryotes, metabarcoding, rrna, taxonomy
- Language: R
- Homepage:
- Size: 760 MB
- Stars: 78
- Watchers: 12
- Forks: 7
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
- jimsghstars - pr2database/pr2database - Protist Ribosomal Reference database (PR2) - SSU rRNA gene database (R)
README
# Protist Ribosomal Reference database (PR2)
[](https://github.com/pr2database/pr2database/releases)
[](https://twitter.com/intent/tweet?text=PR2%20database&url=https://github.com/vaulot/pr2_database&hashtags=PR2database)
## SSU rRNA gene database
The [PR2 database](https://pr2-database.org/) was initiated
in 2010 in the frame of the BioMarks project from work that had
developed in the previous ten years in the Plankton Group of the Station
Biologique of Roscoff. Its aim is to provide a reference database of
carefully annotated 18S rRNA sequences using eight unique taxonomic
fields (from domain to species). At present it contains about 220,000
sequences. A number of metadata fields are available for many sequences,
including geo-localisation, whether it originates from a culture or a
natural sample, host type etc… The annotation of PR2 is performed by
experts from each taxonomic groups. One very important project in this
respect is [EukRef](https://pr2-database.org/eukref/about/) which has
recently decided to merge its effort with PR2. EukRef has
built bioinformatics pipelines that have been used during three
workshops dedicated to specific taxonomic groups.
## Current version
- Version: [5.0.0](https://github.com/pr2database/pr2database/releases)
- Released: 2023-04-06
- DOI: [10.5281/zenodo.7805244](https://doi.org/10.5281/zenodo.7805244)
## Accessing PR2
- [Web interface](https://app.pr2-database.org)
- [Flat files - latest
release](https://github.com/pr2database/pr2database/releases)
- [R package](https://pr2database.github.io/pr2database/index.html)
## About PR2
- [Documentation](https://pr2-database.org/#documentation)
- [Statistics](https://pr2database.github.io/pr2database/articles/pr2_01_stats.html)
## Core Team
- [Daniel VAULOT](mailto:[email protected]), Asian School of the
Environment, Nanyang Technological University, SINGAPORE
- [Javier del CAMPO](mailto:[email protected]), University of
Miami, USA
## Scientific committee and contributors
- [PR2 team](https://pr2-database.org/team/)
## Please cite
- Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L.,
Boutte, C. et al. 2013. [The Protist Ribosomal Reference database
(PR2): a catalog of unicellular eukaryote Small Sub-Unit
rRNA sequences with curated
taxonomy](http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gks1160).
Nucleic Acids Res. 41:D597–604.
## Related Projects
#### 18S rRNA primer database
The [PR2 primer database](https://app.pr2-primers.org/) is a
compilation of primers found in the litterature with an *in silico*
analysis against the PR2 database.
#### metaPR2
The [metaPR2 metabarcode database](https://shiny.metapr2.org)
is a compilation of metabarcode datasets processed by the dada2 R
package and assigned against PR2.
## Questions ?
- Register to our [element.io discussion
board](https://matrix.to/#/#pr2-database:matrix.org)
## Report issues
- Please report any issue on
[GitHub](https://github.com/vaulot/pr2_database/issues)