NXTRIM(1)

✨ NAME ✨

nxtrim — <short_description> 💖 (yes bestie the manpage literally ships a placeholder there, we're keeping it, no cap)

🌸 SYNOPSIS 🌸

nxtrim -1 R1.fastq.gz -2 R2.fastq.gz [options]

🦋 DESCRIPTION 🦋

okay so. the tea:

• Program: nxtrim
• Version: v0.4.3
• Contact: joconnell@illumina.com

that's the whole vibe check. it does the thing. you give it your reads, it gives you trimmed reads. slay. 💅

👑 COPYRIGHT 👑

Copyright © 2016, Illumina, Inc. All rights reserved.</p> see LICENSE for further details, bestie — go read it, it's giving legally binding. 🎀

🫶 Required arguments: (you literally cannot skip these, fr fr)

• -1 [--r1] arg — read 1, in fastq format (gzip is allowed, we're not monsters) 💖
• -2 [--r2] arg — read 2, in fastq format (gzip allowed here too, obviously) 💖

✨ Allowed options: (the fun part)

• -O [--output-prefix] arg — the output prefix. name your babies. 🍼
• --justmp — just creates a the mp/unknown libraries. reads with adapter at the start get completely N masked. not a little masked. fully. N'd out. 😭
• --stdout — print trimmed reads to stdout (it's literally equivalent to justmp)
• --stdout-mp — print only known MP reads to stdout. good for scaffolding, iykyk. 🏗️
• --stdout-un — print only unknown reads to stdout. the mystery reads get their own spotlight 🕵️
• --rf — leave mate pair reads in RF orientation. by default they get flipped into FR. don't ask me why, that's just the default. 🌈
• --preserve-mp — preserve MPs even when the corresponding PE has longer reads. loyalty. 💜
• --ignorePF — ignore chastity/purity filters in read headers. wild behaviour but ok 🙈
• --separate — output paired reads in separate files (prefix_R1/prefix_r2). default is interleaved. pick your fighter. ⚔️
• -a, --aggressive — more aggressive adapter search (see docs/adapter.md). she's coming for every adapter. 🔥
• -s, --similarity arg (=0.85) — the minimum similarity between strings to be considered a match. it's Hamming distance divided by string length, periodt. 📏
• -v, --minoverlap arg (=12) — the minimum overlap to be considered for matching. 12 is the default, that's the bar. 🎯
• -l, --minlength arg (=21) — the minimum read length to output. smaller reads will be filtered. sorry tiny reads, it's not personal. ✂️

💜 AUTHOR 💜

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. iconic of him honestly. 🫶

okay that's the whole page bestie, go forth and trim 🌸💖✨

signing off: this is nxtrim 0.4.3, dated April 2021, manual page NXTRIM(1) — main character energy only, mwah 💅🎀