Provided by: rtax_0.984-3_all 
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)