NAME

       rdp_classifier - taxonomic assignment from next generation sequencing

USAGE:

       rdp_classifier [-f <arg>] [-g <arg>] [-o <arg>] [-q <arg>] [-t <arg>] [-w <arg>]

DESCRIPTION

       The  RDP Classifier is a nave Bayesian classifier that can rapidly and accurately provides
       taxonomic assignments from domain to genus, with confidence estimates for each assignment.

       -f,--format <arg>
              all  tab  delimited  output  format:  [allrank|fixrank|db].  Default  is   allrank.
              allrank:  outputs  the  results  for  all ranks applied for each sequence: seqname,
              orientation, taxon name, rank, conf, ...  fixrank: only  outputs  the  results  for
              fixed  ranks  in order: domain, phylum, class, order, family, genus db: outputs the
              seqname, trainset_no, tax_id, conf. This is good for storing in a database

       -g,--gene <arg>
              16srrna|fungallsu, the default training model for 16S rRNA  or  Fungal  LSU  genes.
              This option will be overwritten by --train_propfile option

       -o,--outputFile <arg>
              output file name for classification assignment

       -q,--queryFile <arg>
              query  file  contains sequences in one of the following formats: Fasta, Genbank and
              EMBL

       -t,--train_propfile <arg>
              specify a property file contains the mapping of the training files if it's  located
              outside of data/classifier/.  Note: the training files and the property file should
              be  in   the   same   directory.    The   default   property   file   is   set   to
              data/classifier/16srrna/rRNAClassifier.properties.

       -w,--minWords <arg>
              minimum  number  of  words  for  each bootstrap trial, Default is 1/8 of the words.
              Minimum is 5

AUTHOR

       This  manual  page  was  generated  using  help2man  and   polished   by   Andreas   Tille
       <tille@debian.org>, for the Debian project (but may be used by others).