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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.

DOE
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 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.

ANNOUNCEMENTS

Pyro News

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

05/23/2014  Informatics Professional job opening at RDP
Work with a team developing important bioinformatics resources.

05/16/2014  Tree Builder Java applet fix in the works
Some problems displaying and interacting with Tree Builder results have been addressed

05/16/2014  RDP staff at ASM, Boston
Poster at 10:45 Sun. morning; ASMCUE workshop info online

05/14/2014  The RDP Paired-end Reads Assembler
The RDP Paired-end Reads Assembler is available for download at RDP Resources page

05/14/2014   Fungal ITS training set
The Fungal ITS training set available for download on RDP Resources page

05/07/2014  FrameBot speed improved
The speed of the FrameBot increased by one to two orders of magnitude

Questions/comments: rdpstaff@msu.edu

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