metaPR2

A database of 18S rRNA metabarcodes

Version: 3.0.0

• Data sets: 67
• Samples: 7 766
• ASVs clustered: 94 373
• ASVs unclustered: 113 989

Release date: 2023-09-26

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:

1. Using a web interface.

2. Run as docker container. <= This is the best way

3. Download the R package and launch the shiny application (hardest).

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://shiny.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 or Windows Powershell)

# Download container
docker pull vaulot/metapr2:latest

# Launch container
docker run --rm -p 8080:8080 vaulot/metapr2

• In your browser: http://localhost:8080/

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("qs", version = "0.27.3")
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()

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$^{2}$: 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