QUORUM_ERROR_CORRECT_READS(1)

👑 QUORUM_ERROR_CORRECT_READS 👑

okay bestie, so this is a page from section 1 of the User Commands manual — it's quorum_error_correct_reads, and she is that girl. 💅 Let me tell you everything she does, no gatekeeping.

✨ NAME ✨

quorum_error_correct_reads — error correct reads from a fastq file based on the k-mer frequencies 🌸

like, she reads your fastq and she fixes it. based on how often the k-mers show up. that's the whole vibe. 🦋

🎀 SYNOPSIS 🎀

error_correct_reads [options] db:path sequence:path+

so yeah, options first (they're all optional, she's chill), then a db:path — that's your k-mer database, she needs it — and then sequence:path+, which means one or more sequence paths. the + is doing so much work there. 💖

💖 DESCRIPTION 💖

Error correct reads from a fastq file based on the k-mer frequencies.

that's it. that's the whole description. she's simple, she's effective, she ate. 🔥

🌈 OPTIONS 🌈

quick heads up before we dive in — the defaults are the little numbers in () and a * means required (there are none here, so you're free, go wild). 🧚

• -t, --thread=uint32 — Number of threads (1). she can multitask but by default she's doing one thing at a time, very mindful of her energy. 🧘
• -m, --min-count=uint32 — Minimum count for a k-mer to be considered "good" (1). below this? not good enough, sorry babe. ✨
• -s, --skip=uint32 — Number of bases to skip for start k-mer (1). she needs a running start, okay? 🏃
• -g, --good=uint32 — Number of good k-mer in a row for anchor (2). two good ones in a row and she's anchored, locked in, no cap. ⚓
• -a, --anchor-count=uint32 — Minimum count for an anchor k-mer (3). the anchor k-mer has standards. 👑
• -w, --window=uint32 — Size of window (10). this is her little viewing window, like a magnifying glass on the read. 🔍
• -e, --error=uint32 — Maximum number of error in a window (3). more than this and the vibe check fails. 💀
• -o, --output=prefix — Output file prefix (error_corrected). she names her files error_corrected, iconic, no notes. 🎀
• --contaminant=path — Jellyfish database of contaminant k-mers. for sniffing out the uninvited guests at the party. 🦠
• --trim-contaminant — Trim reads containing contaminated k-mers instead of discarding (false). so instead of ghosting the whole read, she just snips the icky part out. ✂️
• --homo-trim=int32 — Trim homo-polymer run at the 3' end. yes she will trim that run. the 3' end specifically. respect the 3' end. 💜
• --gzip — Gzip output file (false). compress that output, we love a space-saver. 🗜️
• -M, --no-mmap — Do not memory map the input mer database (false). by default she does memory map it, so use this if you want her to not do that. 🗺️
• --apriori-error-rate=double — Probability of a base being an error (0.01). a little faith, a little math. 📊
• --poisson-threshold=double — Error probability threshold in Poisson test (1.0e-06). yes, Poisson like the distribution, she's academic AND cute. 🎓
• -p, --cutoff=uint32 — Poisson cutoff when there are multiple choices. for when she's indecisive and needs a rule. 🤔
• -q, --qual-cutoff-value=uint32 — Any base above with quality equal or greater is untouched when there are multiple choices. so, good-quality bases get left alone, she's not gonna mess with them. 🙅
• -Q, --qual-cutoff-char=string — Any base above with quality equal or greater is untouched when there are multiple choices. same energy, but as a character instead of a value. 💅
• -d, --no-discard — Do not discard reads, output a single N (false). she keeps everything, she just leaves a lil N as a souvenir. 🌸
• -v, --verbose — Be verbose (false). she will tell you everything that's happening. girl loves to talk. 🗣️
• -U, --usage — Usage. just the usage, the quick rundown. ⭐
• -h, --help — This message. hi bestie, here's the help. 🫶
• -V, --version — Version. she'll tell you what version she is, she's honest like that. 💖

quick reminder: don't get any of these flags twisted, -q and -Q are two different girls and they take two different kinds of argument. lowercase is a uint32, uppercase is a string. iykyk. 😭

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. ✨

okay that's the whole page bestie, you're officially caught up. and just so you know who to credit — this is quorum_error_correct_reads 1.1.1, dated May 2017, straight out of the User Commands manual. periodt. 💅🎀🦋