This is the command rdp_classifier that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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