NAME

       rtax  -  Rapid  and  accurate  taxonomic  classification  of short paired-end sequence reads from the 16S
       ribosomal RNA gene

SYNOPSIS

       rtax [OPTION]...

DESCRIPTION

OPTIONS

       -r refd      reference database in FASTA format

       -t taxonomy  taxonomy file with sequence IDs matching the reference database

       -a queryA    FASTA file containing query sequences (single-ended or read 1)

       -b queryB    FASTA file containing query sequences (read b, with matching IDs)

       -x           Reverse-complement query A sequences (required if they are provided in the reverse sense)

       -y           Reverse-complement query B sequences (required if they are provided in the reverse sense)

       -i regex     regular expression used to select part of the fasta  header  to  use  as  the  sequence  id.
                    Default: "(\S+)"

       -l file      text file containing sequence IDs to process, one per line

       -d delimiter delimiter separating the two reads when provided in a single file

       -m tempdir   temporary  directory.   Will be removed on successful completion, but likely not if there is
                    an error

       -f           for sequences where only one read is available, fall back  to  single-ended  classification.
                    Default: drop these sequences

       -g           for  sequences  where  one  read  is  overly  generic,  do  not  fall  back  to single-ended
                    classification.  Default: classify these sequences based on only the more specific read

       -o classifications.out
                    output path

EXAMPLES

       A quickstart example can be found here: https://github.com/davidsoergel/rtax/wiki/QuickStart

       Rtax  can  also   be   used   within   QIIME   workflows,   see   this   link   for   more   information:
       http://www.qiime.org/tutorials/rtax.html

AUTHOR

       This manual page was written by Simon Kainz <simon@familiekainz.at> for the rtax package.

       Rtax was written by David A. W. Soergel <soergel@cs.umass.edu>.

                                                   27 Nov 2014                                           rtax(1)