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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.


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 extremely large datasets, please use our command line tools, available through 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

03/26/2014  Informatics Professional job opening at RDP
Work with a team developing important bioinformatics resources.

03/19/2014  All services should be back online!
Sorry for the interruption.

03/19/2014  RDP Site Issues
Some services temporarily unavailable.

03/07/2014  RDP Release 11.2
RDP Release 11.2 features updated Fungal 28S LSU hierarchy model

11/08/2013  RDPipeline Bug Fix
Some users were experience issues with the complete linkage clustering tool when uploading files with names containing a space. The RDPipeline wil...

11/08/2013  Fungene Repository Release 7.3
Release 7.3 of the Functional Gene Repository is now live at This release includes a new gene, nxrB, and updated with ...

10/16/2013  RDP 11 and RDPipeline are now live
RDP 11 and the new RDP Pipeline for Amplicon Sequences (RDPipeline) are now live and available to researchers.

10/16/2013  RDP 11 Major Release Tonight
RDP sites will be down this evening for new release deployment

10/09/2013  FunGene article published
The article describing our FunGene data and tools is published in Frontier in Microbiolgy.

10/09/2013  RDP FrameBot article published
The article describing RDP FrameBot (a frameshift correction tool) is published in the journal mBio


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