YANAGIBA(1)

📦 version 1.0.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 YANAGIBA 💖

okay bestie, sit down, hydrate, and let me tell you about yanagiba — she's a little command-line queen who filters low quality Oxford Nanopore reads that got basecalled with Albacore. that's the whole vibe. that's her whole thing. 🧬✨

🌸 SYNOPSIS 🌸

usage: yanagiba [-h] -i INFILE [-s SUMMARYFILE] [-o OUTFILE] [-l MINLEN]
                [-q MINQUAL] [--headtrim HEADTRIM] [--tailtrim TAILTRIM] [-u]

like yes, that's a lot of brackets, breathe. it's giving "options are your friend". 💅

🦋 DESCRIPTION 🦋

so here's the tea, bestie: yanagiba filters and slices Nanopore reads which have been basecalled with Albacore. no cap. it takes a fastq.gz and an Albacore summary file and it does its little magic on them. that's it, that's the whole job, and she does it flawlessly, periodt. 🎀

✨ optional arguments ✨

  • -h, --help — shows this help message and then dips (exits). the classic. 🙈
  • -i INFILE, --infile INFILE — your input fastq.gz file. yes queen, gimme the data. 📥
  • -s SUMMARYFILE, --summaryfile SUMMARYFILE — the Albacore summary file, and it must have a header row. don't skip the header bestie, she will not vibe with that. 📋
  • -o OUTFILE, --outfile OUTFILE — writes your filtered reads into this file in .bgz format. that's the format. that's the assignment. 💾
  • -l MINLEN, --minlen MINLEN — excludes reads shorter than this length. bye-bye tiny reads, we don't know them. Default: 0 ⭐
  • -q MINQUAL, --minqual MINQUAL — the minimum quality score needed to retain a read. if it doesn't hit the bar, it's not making the cut. Default: 10 🔥
  • --headtrim HEADTRIM — trims x bases off the beginning of each read. snip snip. ✂️ Default: 0
  • --tailtrim TAILTRIM — trims x bases off the end of each read. also snip snip, other side. ✂️ Default: None
  • -u, --forceunique — enforces unique reads. it only stores the first instance of a read from the fastq input when a readID shows up multiple times. one read, one entry, no duplicates invited to the party. 👑💀

🫶 AUTHOR 🫶

this manpage was written by Nilesh Patra for the Debian distribution, and honestly? iconic of them. it can be used for any other usage of the program too, so go wild. 🌈

and that's the whole page bestie!! 💜 this is yanagiba version 1.0.0, from way back in June 2020 — a true vintage queen who still slays. go filter some reads, you got this. 🎀✨🦋🌸💖

📦 where this page comes from