RDP Classifier (original) (raw)
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/).
Citation:
1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7.
2. Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc. 2024 Apr 11;13(4):e0106323.
Features
- The RDP Classifier 2.14 released in August 2023 contains the latest bacterial and archaeal taxonomy training set No. 19. See publication Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. https://doi.org/10.1128/mra.01063-23
- Release 2.11 provides subcommand to display the pre-compiled taxonomy versions.
- Release 2.10 provides gene copy number adjustment for 16S gene sequences.
- Release 2.7 offers updated Fungal LSU training set No 11. The new Fungal LSU training set offers increased coverage of the Glomeromycota, Chytridiomycota and other basal lineages, with expanded non-fungal Eukarya phyla to better separate fungi from other eukaryotes.
- The RDP Classifier now allows classification of both bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences.
- The RDP MultiClassifier has been merged with RDP Classifier as one single package. The new version of RDP Classifier now offers subcommands for classification, library comparing, retraining classifier, leave-one-out testing and cross validation. See instructions on https://github.com/rdpstaff/classifier.
License
GNU General Public License version 2.0 (GPLv2)
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