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COMMAND(1) |
User Commands |
COMMAND(1) |
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).