New article on #protist global distributions combining the #Mixoplankton and #metaPR2 databases with revised functional annotations led by @lusantof.bsky.social, Michaela E. Larsson, and Suzana Leles with Aditee Mitra and Emile Faure. Now available on Ocean Microbiology
rdcu.be/fanlx
Docker containers are now available for the three PR2 applications:
- pr2-database: reférence database
- pr2-primers: primer database and analysis
- metapr2: metabarcode database and visualization.
This by far the easiest way to use these databases on your computer.
hub.docker.com/repositories...
For those of you who are using metaPR2 extensively, a good alternative to installing the R package which can cause trouble because of dependencies, you can try the newly available docker container:
hub.docker.com/repository/d...
Using the PR2 database...
PR2 primers version 2.1.0 has been released. This does not include any new primer, but now the database uses the latest version of PR2 (5.1.1) to perform in silico analyses.
Access here: app.pr2-primers.org
Version 5.1.1 of the PR2 database has been released.
The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations
metaPR2 version 3.0 has just been released.
Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.
app.metapr2.org
Javier is the co-coordinaror of PR2... Warn congratulations.
A paper using the PR2 and metaPR2 database.
Nice paper making use of PR2
@daniel-vaulot.bsky.social presenting the @pr2-database.bsky.social at our DNA metabarcoding course at @biovitenskap.bsky.social A very good new addition to our biannual course 👏
Grateful I got the opportunity to contribute to this amazing resource #ProtistsOnSky
I am very happy that ROD (The Ribosomal Operon Database) is now included in the outstanding PR2 web interface, enhancing its accessibility and utility. I hope to make some updates to ROD in the near future. with @drhyfe.bsky.social
Some functional traits have been added:
- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021
A few taxonomic groups have been updated from work performed during the 2023 Barcelona EukRef workshop and from individual contributions including:
- Picozoa
- Choropicophyceae
- Rhodophyta
- Dinophyceae
- Foraminifera
- The web interface now provides access to the ROD database that contains full-length eukaryotic ribosomal operons developed by @krabberod.bsky.social
Announcing the new release of the PR2 database, version 5.1.
pr2-database.org/post/news/20...
Very big thanks to all the contributors: @fonamental.bsky.social @ambonacolta.bsky.social @krabberod.bsky.social and more...
A few highlights:
We are back on-line. It took less time than anticipated to upgrade R....
The PR2, metaPR2 and PR2-primers websites will be off in the coming days as we are switching from R 3.6 to R 4.4.
Protists are not just sequences, they have incredible shapes...
New paper using PR2.
Looks like a very good tool to use with the PR2 database.
Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...
A tool to use with the metaPR2 datasets ?
All PR2 shiny servers are back up and running...
