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:
       http://dev.davidsoergel.com/trac/rtax/wiki/QuickStart

       Rtax can also be  used  within  QIIME  workflows,  se  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 2013                                    rtax(1)