UNICYCLER_SCRUB(1)

✨ NAME ✨

unicycler_scrub — read trimming, chimera detection and misassembly detection 💖

Okay so this is a User Commands page (that's section 1 in manpage-land, iykyk) and it's literally the little scrubby scrubber that cleans up your reads and your assemblies. Bestie, it trims, it detects chimeras, it detects misassemblies — it's giving full glow-up for your sequences 🧚✨

🌸 SYNOPSIS 🌸

unicycler_scrub [-h] -i INPUT -o OUT [-r READS] [--trim TRIM] [--split
SPLIT] [--min_split_size MIN_SPLIT_SIZE] [--discard_chimeras] [-t
THREADS] [--keep_paf] [--parameters PARAMETERS] [--verbosity VERBOSITY]

🦋 DESCRIPTION 🦋

Unicycler-scrub — read trimming, chimera detection and misassembly detection. That's the whole vibe. It scrubs. It trims. It catches chimeras and misassemblies. Periodt 💅

👑 OPTIONS 👑

• -h, --help — show this help message and exit. The classic. The icon. When in doubt, ask for help 🫶
• -i INPUT, --input INPUT — these are the reads or the assembly that's getting scrubbed (can be FASTA or FASTQ format, bestie). This is the thing you're cleaning up ✨
• -o OUT, --out OUT — the scrubbed reads or assembly get saved to this file (and it'll have the same format as the --input file's format, no cap). Orrr you can use "none" if you don't want an output file at all 🙈
• -r READS, --reads READS — these are the reads used to scrub --input (can be FASTA or FASTQ format). Default: the same file as --input 💫
• --trim TRIM — how aggressive the trimming is gonna be, from 0 to 100, where 0 is literally no trimming and 100 is very aggressive trimming. Default: 50 ✂️
• --split SPLIT — how aggressive the splitting is, from 0 to 100, where 0 is no splitting and 100 is very aggressive splitting. Default: 50 🪓
• --min_split_size MIN_SPLIT_SIZE — parts of split sequences only get outputted if they're at least this big. Default: 1000 📏
• --discard_chimeras — if you use this, chimeric sequences get discarded instead of split. Default: False 💀
• -t THREADS, --threads THREADS — number of threads used. Default: 4 ⚡
• --keep_paf — saves the alignments to file, which makes repeated runs faster because the alignments can be loaded from file. Default: False 💾
• --parameters PARAMETERS — low-level parameters, and listen, this is for debugging use only, okay? Do not go poking around in there for fun. Default: (empty) 🙈
• --verbosity VERBOSITY — level of stdout information. Default: 1 🗣️
  • 0 = no stdout
  • 1 = basic progress indicators
  • 2 = extra info
  • 3 = debugging info

🎀 SEE ALSO 🎀

unicycler(1) — go say hi to the main character of the family 🌈

💜 AUTHOR 💜

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

And that's a wrap, bestie — this page is unicycler_scrub version 0.4.7, dated October 2018. Slay 💅✨