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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 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.

ANNOUNCEMENTS

Pyro News

11/10/2017  myRDP login problem fixed!

05/16/2017  Apology for slow/NO connection to RDP tools today
Thanks to Alex/Brian, etc. for working things out in the server room

05/10/2017  RDP Director at GSC 19, May 14-17
Genomic Standards Consortium Meeting, Brisbane, Queensland, Australia

05/10/2017  Possible Friday, May 12, morning interruptions
Emergency Generator Testing from 9-10 A.M.

12/13/2016  Most Highly Cited Researchers
Congratulations to RDP Director James Cole

09/30/2016  RDP Release 11.5 available
Updated 16S rRNA training set to training set No. 16.

08/16/2016  Possible Friday morning interruptions
Building electrical testing/maintenance

06/30/2016  RDP Classifier Updates
The Classifier 16S training set and Fungal ITS Warcup set have been updated

06/03/2016  RDP staff on the road!
Teaching in China, Genomic Standards Consortium meeting in Crete, special ASM Microbe events in Boston

10/07/2015  Xander assembler article is published.
Xander: Employing a Novel Method for Efficient Gene-Targeted Metagenomic Assembly

Questions/comments: rdpstaff@msu.edu

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