metaPR2 version 4.0.0
We are very pleased to announce version 4.0.0 of the metapr2 database.
Accessing the metapr2 database
- Web interface: https://app.metapr2.org
- Docker container
- R package
The full metapr2 dataset can now be directly downloaded from the Zenodo record. Two files are available
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)
Content of the database
This version constitutes a major update as it contains 120 new datasets from oceanic, freshwater as well as terrestrial environments.
- Data sets: 187
- Samples: 26 315
- ASVs clustered: 229 793
- ASVs non clustered: 275 680
It 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).
ASVs are assigned with PR2 database version 5.1.
More information here
A word of caution
Since this release contains a very large number of samples and metabarcodes (ASVs), we encourage you to select a small number of samples, typically less than 3000. Additionally rather than using the interactive web application we encourage you to download and install the application on your computer using docker.
Issues/Problems
Please let us know of any problem you encounter with this release on GitHub.
