A database of 18S rRNA metabarcodes
Release date: 2026-07-01
Version: 4.0.0
- Data sets: 187
- Samples: 26 315
- ASVs clustered: 229 793
- ASVs non clustered: 275 680
- This release (4.0) includes all EukBank datasets that contained more than 20 samples (Berney, C., Mahé, F., Henry, N., Lara, E., de Vargas, C., & consortium, E. (2023). EukBank 18S V4 dataset. Zenodo. https://doi.org/10.5281/zenodo.7804946).
Presentation
MetaPR2 is a database of published 18S rRNA metabarcodes that have been reprocessed and assigned using PR2.
Acessing the database
Access to the database to map, search and download the barcodes can be done in three different ways:
Using a web interface.
Run as docker container. <= This is the best way
Download the R package and launch the shiny application (hardest).
Download raw data and process them with your scripts (R, Python or other)
Please privilege method # 2 (Docker Image) if you are going to use metapr2 extensively or for a course as the server will crash if too many users are logged.
1 - Web interface
- Launch in your browser: http://app.metapr2.org
- Help : https://pr2database.github.io/metapr2-shiny/articles/
2 - metaPR2 Docker container (Easier)
Available from Docker repository
Install docker on your computer: https://docs.docker.com/desktop/
At shell prompt (can be Linux, Mac or Windows Powershell). Note that a Powershell window can be opened from RStudio Terminal or VSCode Terminal.
# Download container
docker pull vaulot/metapr2:latest
# Launch container
docker run --rm -p 8080:8080 vaulot/metapr2- In your browser: http://localhost:8080/
- To exit type CTRL-C in the shell prompt
3 - metaPR2 shiny R package (Harder)
Note: You may run into trouble because quite a few packages need to be installed.
3.1 - Install the R package from GitHub
- Launch R or R Studio
- Run the following lines.You may have to install some CRAN packages required by metapr2 if they are not installed on your machine.
install.packages("devtools")
install.packages("remotes")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
remotes::install_version("blaster", version = "1.0.7")
BiocManager::install("phyloseq")
BiocManager::install("Biostrings")
devtools::install_github("pr2database/metapr2-shiny")3.2 - Launch shiny interface with function run_app()
metapr2::run_app()4 - Download raw data
Data are available from the Zenodo record. You can use your own scripts to process the data.
Two files are provided:
1 - metapr2_4.0_datasets_samples_asv.zip which contains 4 files
- datasets.xlsx - Information on the different datasets selected including reference and GenBank id
- samples.xlsx - List of samples selected with medadata
- asv.xlsx - ASV selected with taxonomy and sequence
- asv.fasta - ASV selected with taxonomy and sequence in fasta form
2 - metapr2_4.0_asv_abundance.tsv.gz - Percent of reads (normalized to total number of eukaryotic reads in the sample), for each ASV and each sample (long form). The file_code and asv_code columns link this table to the samples and asv tables (samples.xlsx and asv.xlsx)
Help
Extensive help is provided here.
Errors
Please report errors in the Issues page of the metaPR2 database.
Citation
Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources 22, 3188–3201. https://doi.org/10.1111/1755-0998.13674
Resources
Website: https://shiny.metapr2.org/
Source code: https://github.com/pr2database/metapr2-shiny
Maintainer
- Daniel Vaulot: vaulot@gmail.com
Contributors
- Daniel Vaulot, CNRS Roscoff, U. of Oslo
- Adriana Lopes dos Santos, U. of Oslo
- Clarence Sim, NTU-ASE Geek lab
- Denise Ong, U. of Oslo
- Bryan Teo, NTU-ASE Geek lab
- Charlie Biwer, Uppsala University Sweden
- Mahwash Jamy, Uppsala University Sweden
- EukBank core team (Frédric Mahé, Nicolas Henry, Cédric Berney)