joey711/phyloseq — Issue #35: Add importer for RDP multclassifier
Author: joey711
Created: 2011-10-19 18:53:00+00:00
State: open
Labels: Feature

http://rdp.cme.msu.edu/classifier/classifier.jsp

This is a potential alternative-branch / addition of the RDP pipeline, wherein raw sequences are preprocessed by RDP pipeline, but the classification/clustering is performed by the multclassifier on a user's local machine. The output will be different, and should include taxonomic classification data similar in nature to the output from pyrotagger.

I have not yet tested multclassifier to verify that its performance / output is appropriate for phyloseq. This should not be too difficult to do, and might add an extra feature on the RDP side. For the moment, only the RDP clust file appears to be appropriate for phyloseq import, and this can only create an otuTable (OTU abundance table), as the related data types are absent from the pipeline.