Contents

Web-based Workflows:

Processing 16S rRNA data using an unsupervised method

Processing 16S rRNA data using a supervised method

Processing Functional Gene Data using an unsupervised method

Individual Web-based Tools:

Using the Pipeline Initial Process

Using the Paired-End Reads Assembler

Using RDP Classifier

Align 16S rRNA sequences using Infernal Aligner

Performing Complete Linkage Clustering

--Using the .clust Results File (for abundance stats, diversity stats, OTU matrix or rarefaction)

Align protein sequences using HMMER3 Aligner

Frameshift-correction and closest match assignment by RDP FrameBot

Running the Defined Community Analysis

Command-line Workflows:

Command-line RDPTools with R/Bioconductor package Phyloseq

Individual Command-line Tools:

See our GitHub README files for

PANDASeq -- coming soon

Miscellaneous:

Running the FASTQ Tool