# RDP-classifier-training-sets

**Repository Path**: kai-ma/RDP-classifier-training-sets

## Basic Information

- **Project Name**: RDP-classifier-training-sets
- **Description**: RDP classifier training set, including bacteria archaea eukaryotes and fungi.
- **Primary Language**: R
- **License**: GPL-2.0
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-07-28
- **Last Updated**: 2024-08-07

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# RDP-classifier-training-sets

The [RDP native training sets](http://rdp.cme.msu.edu/classifier/classifier.jsp;jsessionid=49C6531478DD4D70648EC6FC695B8EA3.10.0.0.9) were commonly employed for amplicon classification of bacteria and archaea. Here, the SILVA's RDP training sets were trained as supplements to the absence of taxonomic information if necessary. The latest SILVA reference sequence sets [(v138)](https://www.arb-silva.de/no_cache/download/archive/release_138/), including bacteria, archaea and eukaryotes, have been reformatted for using the RDP classifier [(v2.13)](https://sourceforge.net/projects/rdp-classifier/). The latest [Unite + INSD](https://unite.ut.ee/repository.php) reference sequences (29.11.2022) were also trained to unify the workflow interface.

Training sets and reference sequences are available at [https://github.com/KaiMa-endeavour/RDP-classifier-training-sets/releases](https://github.com/KaiMa-endeavour/RDP-classifier-training-sets/releases).

## Training sets overview
|Sources|Taxonomic objects|Number of unique sequences|Ranks|
|:----:|:----:|:----:|:----:|
|native RDP|Bacteria|2833748|domain, phylum, class, order, family, genus|
|native RDP|Archaea|145117|domain, phylum, class, order, family, genus|
|SILVA v138|Bacteria|1599148|domain, phylum, class, order, family, genus|
|SILVA v138|Archaea|62300|domain, phylum, class, order, family, genus|
|SILVA v138|Eukaryotes|149373|domain, kingdom, phylum, class, order, family, genus|
|Unite + INSD|Fungi|5335995|kingdom, phylum, class, order, family, genus, species|

## How to use
```
conda install -c bioconda rdp_classifier
rdp_classifier -Xmx16g classify -t ./training set/rRNAClassifier.properties -o ./rdp_output.txt ./query.fasta
```

The missing fields in the headers were filled with `NA` to align the lineages of each individual and to be compatible with the `rdp_classifier train` function.

## References

Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras-Alfaro, A., Kuske, C. R., & Tiedje, J. M. (2014). Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Research, 42(D1), D633–D642. https://doi.org/10.1093/nar/gkt1244

Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P., Picard, K., Glöckner, F. O., Tedersoo, L., Saar, I., Kõljalg, U., & Abarenkov, K. (2019). The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47(D1), D259–D264. https://doi.org/10.1093/nar/gky1022

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596. https://doi.org/10.1093/nar/gks1219

Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology, 73(16), 5261–5267. https://doi.org/10.1128/AEM.00062-07