NEEDLE-MINIMISER(1)

📦
version 1.0.3 · 4 versions
, in ubuntu resolute, ubuntu stonking

💖 NEEDLE-MINIMISER(1) 💖

okay bestie, sit down, hydrate, and let me tell you about needle-minimiser — she Calculates minimiser for given experiments. periodt. that's the whole job. she's giving efficient, she's giving prefilter, she's giving main character energy in a pipeline. 🧚✨

🌸 NAME 🌸

needle-minimiser — Calculates minimiser for given experiments. yes that's it, that's the whole name, short and iconic. 👑

🎀 POSITIONAL ARGUMENTS 🎀

  • ARGUMENT-1 (List of std::filesystem::path) — bestie, please provide at least one sequence file OR provide one file containing all sequence files with the extension .lst. that's the deal. Default: [].
lowkey do not skip this one, she needs something to chew on, fr fr 🍓

✨ OPTIONS ✨

💅 Basic options:

  • -h, --help — Prints the help page. the og, the classic, the "what do I even type" button. 🙈
  • -hh, --advanced-help — Prints the help page including advanced options. it's giving full lore, not just the trailer.
  • --version — Prints the version information. who is she? what era is she in? this tells you. 💫
  • --copyright — Prints the copyright/license information. legal girlie moment, we respect her. ⚖️
  • --export-help (std::string) — Export the help page information. Value must be one of [html, man]. yep, only those two, don't try to be cute with it, html or man, pick one. 🎀
  • -k, --kmer (unsigned 8 bit integer) — Define k-mer size for the minimisers. Default: 20. Default: 20. (yes, the original says it twice — she's that sure. iconic consistency honestly. 😌)
  • -w, --window (unsigned 32 bit integer) — Define window size for the minimisers. Default: 60. Default: 0. (both defaults are listed, don't ask me why, we simply report the facts bestie 🫶)
  • --shape (unsigned 64 bit integer) — Define a shape for the minimisers by the decimal of a bitvector, where 0 symbolizes a position to be ignored, 1 a position considered. Default: ungapped. Default: 0. so like, 0 = not invited to the party, 1 = VIP section only. 💅
  • --seed (unsigned 64 bit integer) — Define seed for the minimisers. Default: 0. same seed, same vibe, reproducible queen. 🌱
  • -o, --out (std::filesystem::path) — Directory, where output files should be saved. Default: "./". she drops her files right where you're standing unless you tell her otherwise. 🎁
  • -t, --threads (unsigned 8 bit integer) — Number of threads to use. Default: 1. Default: 1. (said twice again — she is committed to the bit.) 🔥
  • --include (std::filesystem::path) — Sequence file containing minimizers, only those minimizers will be considered. Default: "". a lil guest list, only these get in. 🚪
  • --exclude (std::filesystem::path) — Sequence file containing minimizers that should not be stored. Default: "". and this is the block list, bestie. bye. 🙅‍♀️
  • --samples (List of signed 32 bit integer) — Define which samples belong together, sum has to be equal to number of sequence files. Default: Every sequence file is one sample from one experiment. Default: []. so like, group-chat assignment basically. 💬
  • -p, --paired — If set, experiments are paired. Default: Not paired. they're a duo, they come as a set, no third wheeling. 👯
  • --cutoff (List of unsigned 8 bit integer) — Define for each sample, what number of found minimisers should be considered the result of a sequencing error and therefore be ignored. Default: Every sample has anautomatically generated cutoff, which is based on the file size. Default: []. (yes, that word is spelled exactly like that in the original — we preserve the artifact, we do NOT touch it 💀) so it's the "this is just noise, not you, babe" threshold. set it per sample or let her auto-generate it from the file size. ✨
  • --ram — If ram is set and multiple threads are used, the multithreading is more RAM friendly at the cost of being slower. so: kinder to your memory, meaner to your patience. pick your struggle. 😭

🦋 VERSION 🦋

  • Last update: 2024-11-07
  • needle-minimiser version: 1.0.3
  • SeqAn version: 3.4.0

🌈 URL 🌈

https://github.com/seqan/needle

go follow her, she's on github, she's got range. ⭐

  • needle-minimiser Copyright: BSD 3-Clause License
  • Author: Mitra Darvish
  • SeqAn Copyright: 2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
  • In your academic works please cite: Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments; Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, and Knut Reinert; Bioinformatics, Volume 38, Issue 17, 1 September 2022, Pages 4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492
bestie if you use her in a paper and don't cite her… we're gonna have a conversation. be a good academic citizen, cite the queens. 🙏✨

For full copyright and/or warranty information see --copyright.

and that's the whole thing!! 🫶 her name tag says needle-minimiser 1.0.3, she got stamped 2024-11-07, and she's out here being NEEDLE-MINIMISER(1) down in the footer like the legend she is. go calculate some minimisers, slay, hydrate, no cap. 💖🎀🦋🌸

📦 where this page comes from