This repository contains trained reference sets that can be used with the Ribosomal Database Project classifier (Wang et al., 2007) to taxonomically assign Diatom SSU rDNA sequences. The latest releases can be downloaded from https://github.com/terrimporter/SSUdiatomClassifier/releases
This classifier is suitable for classifying diatom SSU sequences to genus or order rank depending on the level of confidence required in the taxonomic assignments. To classify a broader diversity of taxa, there is a Eukaryote 18S reference set available at https://github.com/terrimporter/18SClassifier .
You can cite this repository directly:
Teresita M. Porter. (2020, February 11). SSU Diat.barcode Reference Set For The RDP Classifier (Version v1.0.1). Zenodo. http://doi.org/10.5281/zenodo.4741481
Also, please cite the original diatom barcode database:
Rimet, F., Gusev, E., Kahlert, M., Kelly, M. G., Kulikovskiy, M., Maltsev, Y., … Bouchez, A. (2019). Diat.barcode, an open-access curated barcode library for diatoms. Scientific Reports, 9(1), 15116. doi: 10.1038/s41598-019-51500-6
If you use this reference set with the RDP classifier please also cite:
Wang et al. (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73: 5261.
############ Install the RDP classifier if you need it
# The easiest way to install the RDP classifier v2.13 is using conda
conda install -c bioconda rdp_classifier
# Alternatively, you can install from SourceForge and run with java if you don't use conda
wget https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.13.zip
# decompress it
unzip rdp_classifier_2.13
# record path to classifier.jar ex. /path/to/rdp_classifier_2.13/dist/classifier.jar
############ Get the latest RDP-formatted SSU diatom training set
wget https://github.com/terrimporter/SSUdiatomClassifier/releases/download/v1.0/mydata_trained.tar.gz
# decompress it
tar -xvf mydata_trained.tar.gz
# record the path to the rRNAClassifier.properties file ex. /path/to/mydata_trained/rRNAClassifier.properties
############ Run the RDP Classifier
# If it was installed using conda, run it like this:
rdp_classifier -Xmx8g classify -t /path/to/mydata_trained/rRNAClassifier.properties -o rdp.output query.fasta
# Otherwise run it using java like this:
java -Xmx8g -jar /path/to/rdp_classifier_2.13/classifier.jar -t /path/to/mydata_trained/rRNAClassifie
Created from the INRA R-Syst::diatom v7.1 dataset available at https://data.inra.fr/dataset.xhtml?persistentId=doi%3A10.15454%2FTOMBYZ (Rimet et al., 2016). Sequences were obtained from R-syst::diatom [Feb. 11/20]. This version contains 2962 reference sequences and 1198 taxa at all ranks.
Taxonomic assignment results should be filtered according to their bootstrap support values to reduce false positive assignments. Cutoffs are based on leave-one-sequence-out testing of non-singleton genera. Here we recommend MINIMUM bootstrap cutoffs according to query length and assignment rank. Assuming your query sequences are represented in the reference set, using the cutoffs presented in the first table below should ensure 99% accuracy. If you wish to cast a wider net, you can use the second table below for 95% accuracy.
| Rank | Full | 400 bp | 300 bp | 200 bp | 100 bp |
|---|---|---|---|---|---|
| Domain | 0 | 0 | 0 | 0 | 0 |
| Kingdom | 0 | 0 | 0 | 0 | 0 |
| Subkingdom | 0 | 0 | 0 | 0 | 0 |
| Phylum | 0 | 0 | 0 | 0 | 0 |
| Class | 60 | 60 | 60 | 90 | NA |
| Order | NA | NA | 95 | NA | NA |
| Family | NA | NA | NA | NA | NA |
| Genus | NA | NA | NA | NA | NA |
| Species | NA | NA | NA | NA | NA |
NA = No cutoff available will result in 99% correct assignments
| Rank | Full | 400 bp | 300 bp | 200 bp | 100 bp |
|---|---|---|---|---|---|
| Domain | 0 | 0 | 0 | 0 | 0 |
| Kingdom | 0 | 0 | 0 | 0 | 0 |
| Subkingdom | 0 | 0 | 0 | 0 | 0 |
| Phylum | 0 | 0 | 0 | 0 | 0 |
| Class | 0 | 0 | 0 | 0 | 70 |
| Order | 0 | 0 | 0 | 60 | NA |
| Family | 0 | 50 | 60 | 90 | NA |
| Genus | 80 | 90 | 90 | NA | NA |
| Species | NA | NA | NA | NA | NA |
NA = No cutoff available will result in 95% correct assignments
Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., Bouchez, A. 2016. R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database: baw016.
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology, 73(16), 5261–5267. Available from https://sourceforge.net/projects/rdp-classifier/
We acknowledge support from the Canadian federal Genomics Research & Development Initiative (GRDI), Metagenomics-Based Ecosystem Biomonitoring (Ecobiomics) project.
Last updated: May 6, 2021