---
name: "rtax"
section: "1"
platform: "linux"
package: "rtax"
version: "0.984-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/rtax"
---

# rtax(1)

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

## 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\>.