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Data Processing Steps:

PIPELINE INITIAL PROCESS→ Pipeline Initial Process - Use the pipeline to process sequence libraries or assemble paired-end reads
CLASSIFIER→ RDP Classifier - assign bacterial/archaeal 16S or fungal 28S rRNA sequences to our taxonomical hierarchy.
ALIGNER→ Aligner - align sequences using the fast, secondary-structure aware Infernal aligner.
COMPLETE LINKAGE CLUSTERING→ Complete Linkage Clustering - cluster sequences by the complete-linkage clustering method.

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 (link to https://github.com/rdpstaff).

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

Announcements

Pyro News

01/04/2022 RDP Systems Are Running
RDP and FunGene websites are back online! We experienced a multi-server hardware failure in October that took the sites offline The cause has stil...

10/04/2020 RDP Taxonomy Updated
Now using RDP taxonomy 18. Check the updated release and reinstall any older versions of the rdp classifier to use the new taxonomy.

12/12/2018 RDP and Fungene Pipelines are back online now!
The issues causing long delays in RDP and Fungene Pipelines in the past week have been resolved. Users need to re-submit the jobs for which resul...

12/06/2018 RDP and Fungene Pipeline problems
RDP Pipeline and Fungene Pipeline are currently not working properly due to technical issues. While RDP team is working hard on restoring the servi...

11/14/2018 myRDP and RDP Pipeline back to normal
The issue that caused submitted jobs being delayed in myRDP and RDP Pipeline has been resolved. All service functions are working normally.

06/05/2018 RDP phone system restored
RDP phone service is now back online.

06/04/2018 RDP phone system down
RDP phone system is temporarily out of service!

03/05/2018 RDP web tool problems fixed!

03/05/2018 RDP web tool problems
We apologize for ongoing problems with several RDP web tools. Our team is now working hard to get them fixed!

11/10/2017 myRDP login problem fixed!

Questions/comments: rdpstaff@msu.edu

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