FASTQ-CLIPPER(1)

📦 version 1.1.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 FASTQ-CLIPPER(1) 💖

okay bestie, welcome to User Commands — this is the manual page for fastq-clipper, and yes it's part of ea-utils, and yes it's about to be your new favorite little tool. grab a strawberry 🍓 and let's go.

✨ NAME ✨

fastq-clipper — ea-utils: removes one or more adapter sequences from the fastq file 🧚

🌸 DESCRIPTION 🌸

so like, here's how you call her:

fastq-clipper [options] <fastq-file> <adapters>

she removes one or more adapter sequences from the fastq file. periodt. 💅

the adapter sequences are colon-delimited — like, you separate them with colons, that's just how she likes it.

and the stats? they go to stderr, unless you specify -o. so if you were staring at your terminal like "where are my numbers 😭" — that's why. iykyk.

👑 OPTIONS 👑

  • -h — this help. the "help me bestie" button. iconic behavior honestly 🫶
  • -o FIL — output file. and heads up: when you use this, the stats go to stdout instead. the way that switches up on you 💀
  • -p N — maximum difference percentage, and the default is 10. so like, how different can a match be before she's like "nope, not the adapter" 🙈
  • -m N — minimum clip length, default 1. she's not gonna bother clipping anything shorter than this, no cap.
  • -l N — minimum remaining sequence length, default 15. this is how much sequence you need to have left over after the clipping happens. don't leave her with crumbs ✨
  • -x [N] — extra match length past adapter length. the bracket means N is optional, bestie. here's the tea:
    • N = -1 : search all
    • N = 0 : search only up to adapter length
  • -e — end-of-line. this is the default 💖
  • -b — beginning-of-line. and listen. this one is not supported yet. it's giving "coming soon" energy, so don't come for her if it doesn't work — it literally says so 😭
⚠️ real talk: -b is not supported yet. the manpage says it, so i'm saying it. do not build your whole pipeline around it and then act surprised. 💀

🌈 that's a wrap 🌈

fastq-clipper 1.1.2, from way back in July 2015 — she's an elder but she still ate. go clip something, bestie, you've got this. 🎀🦋⭐

📦 where this page comes from