Current coverage of metapr2

metaPR2

The aim of this project is to make publicly available a database of curated metabarcodes processed with dada2 and for which taxonomy is assigned with PR2.

We have developed an interactive web site (https://shiny.metapr2.org) which allows to visualize, analyze and download the processed data. This includes treemaps of taxonomy, barplots as a function of environmental variables, abundance maps as well as alpha and beta diversity analyses.

Please cite: Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13674

The latest version of the database (1.1) has been released in Spring 2022 and contains 41 public data sets including:

  • Biomarks
  • Blanes Time Series - 2004-2013
  • Malaspina - 2010-2011
  • Ocean Sampling Day - 2014 and 2015
  • Tara Oceans - V4 and V9 - 2009-2012 - The Tara V4 data have been reprocessed with dada2
  • Tara Arctic - V4
  • Many Arctic datasets

The database contains also other non-public data sets from our own work, in particular in the Arctic (Green Edge, MicroPolar). If you are interested please contact me.

Publications

Pelagophyte assemblages of the global ocean display low intraspecific diversity

Project Project

Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies

PDF Project Project

Talks