rtax(1)

📦 version 0.984, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 rtax(1) — the glow-up guide 💖

okay bestie, welcome to the manual page for rtax, from the General Commands Manual girlies. pull up a chair, grab a strawberry 🍓, and let's get into it.

✨ NAME ✨

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

like, it looks at your reads and tells you who they are. taxonomy sleuthing. it's giving forensic scientist but for bacteria 💅

✨ SYNOPSIS ✨

rtax [OPTION]...

that's it. that's the whole vibe. you just throw options at it. no cap.

✨ DESCRIPTION ✨

okay so. the original page literally has the DESCRIPTION heading and then… nothing under it. an empty section. iconic honestly, she said "no thoughts, head empty" 💀 i'm not gonna invent lore for it, so bestie, that's the whole description. moving on. 🙈

✨ OPTIONS ✨

every single flag, right here, no skips, fr fr. ✨

  • -r refd — your reference database, in FASTA format. this is the encyclopedia she's matching against 📚
  • -t taxonomy — the taxonomy file whose sequence IDs match up with the reference database. the reference DB and this file are a matched set, okay, don't split them up 🫶
  • -a queryA — a FASTA file with your query sequences (either single-ended, or read 1 of a pair) 🎀
  • -b queryB — a FASTA file with your query sequences (read b, and the IDs have to match) 👯
  • -x — reverse-complement the query A sequences. required if they came to you in the reverse sense 🔄
  • -y — reverse-complement the query B sequences. required if they came to you in the reverse sense 🔄
  • -i regex — a regular expression used to pick out which part of the FASTA header counts as the sequence ID. Default: "(\S+)" 🔍
  • -l file — a text file listing the sequence IDs to process, one per line 📝
  • -d delimiter — the delimiter that separates the two reads when they're handed to you in a single file ✂️
  • -m tempdir — the temporary directory. it will get removed on successful completion… but lowkey probably not if there's an error, so heads up 😭
  • -f — for sequences where only one read is available, fall back to single-ended classification. Default: drop those sequences 🗑️
  • -g — for sequences where one read is overly generic, do not fall back to single-ended classification. Default: classify those sequences using only the more specific read 🎯
  • -o classifications.out — the output path 💾

✨ EXAMPLES ✨

a quickstart example is living right here, go say hi:

https://github.com/davidsoergel/rtax/wiki/QuickStart

and rtax can also be used inside QIIME workflows — this link has the tea:

http://www.qiime.org/tutorials/rtax.html

✨ AUTHOR ✨

this manual page was written by Simon Kainz <simon@familiekainz.at> for the rtax package. ✍️

and rtax itself was written by David A. W. Soergel <soergel@cs.umass.edu>. 👑

and that's a wrap, bestie!! this page is dated 27 Nov 2014 and it's the rtax(1) page from the General Commands Manual — the source/version and date, served cute, as promised. go classify something. slay 🎀✨💜

📦 where this page comes from