rdp_classifier - taxonomic assignment from next generation
sequencing
rdp_classifier [-f <arg>] [-g <arg>] [-o
<arg>] [-q <arg>] [-t <arg>] [-w <arg>]
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
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).