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).