[ FunGenePipeline | FunGene | RDPipeline | RDP ]

FunGene Pipeline

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Pipeline

PIPELINE→ Pipeline - Run a set of sequences through our standard processing pipeline

Pipeline Tools:

PIPELINE INITIAL PROCESS→ Pipeline Initial Process - Use the RDP Pipeline to process sequence libraries from raw sequencer output to analysis.
DEFINED COMMUNITY ANALYSIS→ Defined Community Analysis - Perform error analysis of a defined community.
DEREPLICATOR→ Dereplicator - Consolidates one or more sequence files to a single sequence file containing only unique sequences. In addition, produces an id and sample mapping to track how many sequences came from which file.
USEARCH CHIMERA CHECK→ Chimera Check - Check amplicon sequence files for chimeras using USEARCH 6.0
FRAMEBOT→ Framebot - Translate nucleotide sequences to protein using Framebot to detect and correct frameshifts in the reads using a set of known sequences.
ALIGNER→ Aligner - Align sequences using HMMER3 aligner.
MCCLUST→ Complete Linkage Clustering - Cluster sequences by the complete-linkage clustering method using RDP's mcClust.
EXPAND MAPPINGS→ Expand Mappings - Expand a dereplicated sequence file back in to multiple files with all duplicate sequences.
REPRESENTATIVE SEQUENCES→ Representative Sequences - Find representative sequences (least distance squared) from a cluster file.
RAREFACTION→ Rarefaction - Calculate Rarefaction from a single sample file.
SHANNON & CHAO1 INDEX→ Shannon & Chao1 Index - Calculate Shannon Index & Chao1 estimator from a single sample file.
JACCARD & SØRENSEN INDEX→ Jaccard and/or Sørensen Indices - Calculate Jaccard and/or Sørensen indices from a cluster/spade tabular style input multi-sample file.

If you use RDP's FunGene, please cite:
Fish, J. A., B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole (2013).
FunGene: the Functional Gene Pipeline and Repository. Front. Microbiol. 4: 291.

Note: If you experience problems with the pyrosequencing pipeline, please contact us and we will help you get your sequences processed.

Fungene 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!