RDP Classifier

RDP Classifier is used to assign sequences derived from bacterial and archaeal 16S genes and fungal 28S gene to the corresponding taxonomy model. The classification algorithm has been published Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. [PMID: 17586664].

RDP provides three ways to run this tool to fit your analysis needs.

1. Run RDP Classifier interactively

Site: http://rdp.cme.msu.edu/classifier/classifier.jsp

Tutorial: Interactive Classifier Tutorial

Features: Web-based job submission and interactive interface for exploring results.

Input requirements:

  • A single FASTA, FASTQ or SFF file
  • ≤ 100K sequences and ≤ 50 MB file size
  • Uncompressed sequence file

2. Run RDP Classifier on RDPipeline

Site: https://pyro.cme.msu.edu/classifier/form.spr

Tutorial: RDPipeline Classifier Tutorial

Features: Web-based job submission and result download using myRDP account.

Input requirements:

  • Single or multiple FASTA, FASTQ or SFF files
  • ≤ 1 million sequences
  • Compressed files recommended

3. Integrate RDP Classifier to your local workflow

Sites:

  1. https://github.com/rdpstaff/classifier
  2. http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/

Tutorial: See README

Features: To be installed locally (all platforms) and run through command-line; readily to integrate into your own analysis workflow.

Input requirements:

  • Single or multiple FASTA, FASTQ or SFF files
  • More options including retraining Classifier and accuracy testing
  • Unlimited number of sequences
  • Uncompressed sequence files

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