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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.
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

03/02/2013 System Maintenance 2013-03-06
All websites will be taken offline Wednesday 5-7pm eastern time for regular system maintenance

12/11/2012 RDP Hardware Upgrades
To keep up with increasing demands on our sites we've added 5 new hosts to the Pyro, Fungene, and CME website cluster.

Additionally we...

11/26/2012 Scheduled site maintenance
The pyro, fungene, and cme websites will be briefly unavailable this afternoon while we perform some routine hardware maintenance. The downtime wi...

11/11/2012 Announcing the new RDP Wiki!
We are pleased to announce the release of the RDP Wiki, available at http://rdp.cme.msu.edu/wiki

10/25/2012 More RDP Tools on github
Links:
FrameBot prebuilt jar on sourceforge
10/23/2012 Fungene release 7.1
Fungene release 7.1 went live tonight, bringing with it updates from genbank release 192 on Oct. 11th

10/15/2012 Pyro job emails issue resolved
We've resolved the ssl certificate issue preventing job emails from being sent. We're working on resending the job completion emails to anyone who...

10/15/2012 No result emails from pyro jobs
There is an issue with the SSL certificate from the MSU mail server preventing our tools from sending result emails.

We apologize for ...

10/12/2012 Maintenance Complete
Hardware upgrades are now complete.

10/12/2012 Server Maintence
The pyro/fungene/cme sties may experience some intermittent downtime as we do some hardware upgrades on the back end servers hosting these sites.