This is the command rtax that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use rtax online using onworks.net services
