QUAL_TRIM.PY(1)

💖 qual_trim.py — the manual page, but make it slay 💖

okay so bestie, welcome to qual_trim.py(1) — yes that's the manual name, no we're not being formal about it. This is the User Commands era of the docs and honestly? iconic.

✨ NAME ✨

qual_trim.py — Perform quality trimming for single-end reads. That's the whole vibe. It trims your reads based on quality. Periodt.

🌸 DESCRIPTION 🌸

lowkey the usage goes like this:

qual_trim.py [-h] [-b BASE] [-p PROB] [-q SCORE] [-l BP] [--illumina5]
             [--solexa]
             FASTQ

and fr fr, what it does is: Perform quality trimming for single-end reads. That's the mission statement, bestie, and it is giving main character energy.

🎀 positional arguments: 🎀

• FASTQ — your input, and she's flexible 💅 — this can be stdin or a compressed file, specifically {zip,gz,tar,bz}. so yes you can just pipe it in, or hand her a zipped-up lil treat. no cap.

🦋 optional arguments: 🦋

• -h, --help — show this help message and exit. the classic. the moment you're lost, she's there 🫶
• -b BASE — ASCII-encoded quality offset, like 33 or 64 for example (default: 33). it's literally telling the program where your quality characters sit on the ASCII map, iykyk.
• -p PROB — error probability cutoff (default: 0.1). how much wrongness are we willing to tolerate before we start chopping? this number decides.
• -q SCORE — quality score cutoff (default: '-p 0.1'). note that the default is literally written as '-p 0.1', so the default quality score cutoff is tied to that probability, not some standalone number. copying it exactly, no editing, that's the rule 💅
• -l BP — minimum read length in bp (default: 16). trim too aggressively and you get tiny sad reads, so this is your floor — anything shorter than this and it's not worth keeping around, bestie.
• --illumina5 — Illumina 1.5+ encoding marked with 'B'. it's giving old-school Illumina, the B is the tell 🧚
• --solexa — Solexa encoding. another encoding option, another era of sequencing history, and she supports it.

heads up: the encodings matter, okay? pick the flag that matches your actual data or the quality numbers will be lying to you. ⭐

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. shoutout Andreas, absolute legend, we love a documented tool 🌈

and that's the whole thing, bestie — qual_trim.py version 1.1, dated March 2020, living her best Debian life. go trim some reads, you got this 💖✨🎀