COMMAND(1)

💖 NAME 💖

rdp_classifier — taxonomic assignment from next generation sequencing 🦋

okay so bestie, this is the RDP Classifier manual page, section 1 (User Commands), and it is literally about to become your new fave. let's go ✨

🌸 USAGE: 🌸

rdp_classifier [-f <arg>] [-g <arg>] [-o <arg>] [-q <arg>] [-t <arg>]
[-w <arg>]

that's the whole vibe, six flags, no drama 💅

✨ DESCRIPTION ✨

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain all the way down to genus, with confidence estimates for each and every assignment. like, it doesn't just tell you what something is, it tells you how sure it is too. main character energy fr fr 👑

🎀 the options 🎀

• -f, --format <arg> — all tab delimited output format: [allrank|fixrank|db]. Default is allrank.
  • allrank: outputs the results for all ranks applied for each sequence: seqname, orientation, taxon name, rank, conf, ... (yes, the ... is real, that's how it's written)
  • fixrank: only outputs the results for fixed ranks in order: domain, phylum, class, order, family, genus
  • db: outputs the seqname, trainset_no, tax_id, conf. this one is good for storing in a database 💾
• -g, --gene <arg> — 16srrna|fungallsu, the default training model for 16S rRNA or Fungal LSU genes. heads up bestie: this option will be overwritten by the --train_propfile option. so don't come crying if it gets ignored 🙈
• -o, --outputFile <arg> — output file name for classification assignment. your results gotta go somewhere 📁
• -q, --queryFile <arg> — query file contains sequences in one of the following formats: Fasta, Genbank and EMBL. three options, all iconic 🌈
• -t, --train_propfile <arg> — specify a property file that contains the mapping of the training files, if it's located outside of data/classifier/.

Note: the training files and the property file should be in the same directory. like, they're a package deal, they travel together 🫶

The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.

• -w, --minWords <arg> — minimum number of words for each bootstrap trial. Default is 1/8 of the words. Minimum is 5. so like, five is the floor, periodt 💅

💜 AUTHOR 💜

This manual page was generated using help2man and polished by Andreas Tille <tille@debian.org>, for the Debian project (but may be used by others). shoutout Andreas, real one 🫡✨

aaaand that's the whole page bestie, you ate it up, no crumbs left 🍓

version 2.5 🌟 dated August 2012 🎀 — yeah she's an elder but she still slays, iykyk 💖