[ FGPipeline Home | FGPR Home | Pyro Home | RDP Home ]

FunGene Pipeline

HOVER over tool menu item for a popup description;
CLICK on the tool menu item to begin working with it.

Pipeline

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

Pipeline Tools:

PIPELINE INITIAL PROCESS→ Pipeline Initial Process - align and Classify your 16S rRNA sequences. Use the RDP Pipeline to process sequence libraries from raw sequencer output to analysis.
MOCK COMMUNITY ANALYSIS→ Mock Community Analysis - Perform error analysis of a mock community sequence run.
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.
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.

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

Fungene News

02/17/2012 Problems with loading, turnaround, jobs aborted?
RDP use has increased over 10-fold since November/December

02/10/2012 MSU Network Slowdown
You may experience slow or no connection to the RDP website

12/01/2011 RDP featured in Science Watch, Dec. 2011
Director James Cole answers questions about the RDP Classifier

11/29/2011 Brief Service Interruption
There was a brief power outage from 16:30-17:45 this evening that caused some issues with the RDP sites. The problem has been resolved and all ser...

06/16/2011 RDP User Jobs Slow Turnaround Update
The RDP pyrosequencing site (http://pyro.cme.msu.edu) has been under heavy usage for the past several days (thank you for using our tools!). How...

05/27/2011 RDP Poster at BAGECO11
The RDP FunGene Pipeline: tools for gene-targeted metagenomics

05/18/2011 RDP Staff attending ASM New Orleans, May 22-25
Visit with RDP staff at the poster session on Tues. afternoon

05/04/2011 RDP aids its users in making SRA submissions
Don't have your own submission account? Please call us when you're ready to submit.

05/04/2011 RDP's MIMARKS (former MIENS) GoogleSheets Ready!
Visit our GoogleSheets Help page for further information

04/07/2011 Latest MIMARKS (formerly MIENS) standards released
'The Genomic Standards Consortium: Bringing Standards to Life for Microbial Ecology' is now published online in ISMEJ