Functional Gene Pipeline and Repository

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FunGene Pipeline

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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 - 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.

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