rtax(1)

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

Section 1 rtax bookworm source

Description

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

rtax [OPTION]...

	-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

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

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>.