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Data Processing Steps:

Formats for Common Programs:

Analysis Tools:

Miscellaneous Utilities:

NCBI/EBI Submission Tools:

RDP's mission and funding:

Part of RDP's mission is to provide support to our users. Email and phone contacts are available on the contacts page.

NIEHS Superfund Research Program

About the RDP Pipeline

RDP's Pipeline aims to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. This site offers tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages.

For large datasets, please use our command line tools, available through RDPTools GitHub.

If you use RDPipeline, please cite our most recent article.

Visit our HELP page (with a topical list) or try our new Procedural Tutorials (with example files).

Problems with the pipeline?
Please contact us and we will help you get your sequences processed.


Pyro News

03/27/2015  FrameBot new option Add de novo to references available
Unique abundant query sequences will be added to the starting reference set if qualifications are met.

02/23/2015  WARNING -- RDP unavailable Sat., March 7th
Building network infrastructure upgrades planned 8 A.M. through 6 P.M.

02/16/2015  Introducing Xander assembler
RDP's new gene-target metagenomic assembler, Xander, is released

10/21/2014  Classifier provides gene copy number adjustment
RDP Classifier provides gene copy number adjustment for 16S gene sequences.

09/17/2014  Using RDPTools Output with Phyloseq
A comprehensive tutorial using RDPTools output with Phyloseq package released

09/17/2014  RDP Release 11.3 available
RDP Release 11.3 features updated 16S rRNA hierarchy model

07/08/2014  UNITE Fungal ITS Classifier training set released
Available on RDP Classifier site, RDP SourceForge and GitHub repository.

07/02/2014  BIOM format support
RDP provides support for BIOM format files

07/01/2014  New Warcup Fungal ITS training set released.
Available on RDP Classifier site, RDP SourceForge and GitHub repository.

06/06/2014  RDP staff at MSA meeting, East Lansing MI
Poster about Fungal Analysis


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