QUORUM(1)

💅 QUORUM 💅

okay so bestie, buckle up 🎀 this is the manual page for quorum, living in the User Commands section of your friendly neighbourhood man pages, and we're in its quorum 1.1.1 era. It runs the quorum error corrector on your fastq files. Let's get into it, no cap. ✨

📖 NAME 📖

quorum — run quorum error corrector on fastq file

📖 DESCRIPTION 📖

(the part that's secretly the synopsis, iykyk)

quorum [options] <fastq> [fastq]

📖 DESCRIPTION (part two, the actual tea) 📖

So like, what it does is: it runs the quorum error corrector on the fastq file you hand it. That's the whole vibe. 💖

But wait, there's a plot twist — if you pass the --paired-files switch, then quorum expects an even number of files on the command line, and each pair of those files is holding pair end reads. 👯

And the output? It's giving two files: <prefix>_1.fa and <prefix>_2.fa, and those contain your error corrected pair end reads. Iconic. 🦋

✨ OPTIONS ✨

so many little switches, and every single one of them matters, bestie. here we go 💅

• -s, --size — the Mer database size. default is 200M 🫶
• -t, --threads — how many threads you wanna throw at it. default is the number of cpus, so it'll go feral on your machine by default 😭
• -p, --prefix — the output prefix. default is quorum_corrected 🌸
• -k, --kmer-len — the kmer length. default is 24 ✨
• -q, --min-q-char — the minimum quality char. usually it's 33 or 64, and it autodetects for you, so slay 💖
• -m, --min-quality — the minimum above -q for a high quality base. default is 5 ⭐
• -w, --window — the window size used for trimming 🔥
• -e, --error — the maximum number of errors allowed in a window 👑
• --min-count — the minimum count for a k-mer to be considered good 🌈
• --skip — number of bases to skip to find the anchor kmer 🧚
• --anchor — number of good kmer in a row for an anchor 💜
• --anchor-count — the minimum count for an anchor kmer 🎀
• --contaminant — contaminant sequences 🙈
• --trim-contaminant — trim sequences that have contaminant mers ✂️
• -d, --no-discard — do not discard reads; instead output a single N. default is false 💀
• -P, --paired-files — preserve mate pairs in two files 👯
• --homo-trim — trim homo-polymer on the 3' end 🌸
• --debug — display debugging information 🐛
• --version — display the version 🏷️
• -h, --help — this message, aka the map to the whole thing 🗺️

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. Respect the author bestie 🫶

okay and that's the whole page!! 💖 you're now fully fluent in quorum, and honestly? main character energy. go correct some reads.

signing off from the quorum 1.1.1 era, dated May 2017 — periodt. 💅✨