.TH "rtax" 1 "27 Nov 2014" .SH "NAME" rtax - Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene .SH "SYNOPSIS" .B rtax [\fIOPTION\fR]... .SH DESCRIPTION .PP .SH OPTIONS .TP 13 .I \-r refd reference database in FASTA format .TP 13 .I \-t taxonomy taxonomy file with sequence IDs matching the reference database .TP 13 .I \-a queryA FASTA file containing query sequences (single-ended or read 1) .TP 13 .I \-b queryB FASTA file containing query sequences (read b, with matching IDs) .TP 13 .I \-x Reverse-complement query A sequences (required if they are provided in the reverse sense) .TP 13 .I \-y Reverse-complement query B sequences (required if they are provided in the reverse sense) .TP 13 .I \-i regex regular expression used to select part of the fasta header to use as the sequence id. Default: "(\\S+)" .TP 13 .I \-l file text file containing sequence IDs to process, one per line .TP 13 .I \-d delimiter delimiter separating the two reads when provided in a single file .TP 13 .I \-m tempdir temporary directory. Will be removed on successful completion, but likely not if there is an error .TP 13 .I \-f for sequences where only one read is available, fall back to single-ended classification. Default: drop these sequences .TP 13 .I \-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 .TP 13 .I \-o classifications.out output path .SH EXAMPLES A quickstart example can be found here: \fIhttps://github.com/davidsoergel/rtax/wiki/QuickStart\fR .P Rtax can also be used within \fIQIIME\fR workflows, see this link for more information: \fIhttp://www.qiime.org/tutorials/rtax.html\fR .SH AUTHOR This manual page was written by Simon Kainz for the rtax package. .P Rtax was written by David A. W. Soergel .