NEEDLE(1)

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

💖 NAME 💖

needle — okay so the original page literally just leaves it at a lil dash and nothing else, which is so mysterious of it, but we move. Bestie, this is needle, and she's here to do big bioinformatics things.

🦋 DESCRIPTION 🦋

Hiii so needle is that girl for two very specific jobs, and she does them with the ibf command or the estimate command:

  • Build an Interleaved Bloom Filter (IBF) — that's the ibf command's whole personality 💅
  • Estimate the expression of transcripts — that's estimate, no cap ✨

Pick your fighter, she doesn't do "both at once", she does "one really well". 😌

🌈 SUBCOMMANDS 🌈

She must be invoked with one of these subcommands, periodt. No subcommand, no service:

  • count
  • delete
  • estimate
  • genome
  • ibf
  • ibfmin
  • insert
  • insertmin
  • minimiser

Every single one of these has its own help page, so if you want the tea, go read the respective one — like, just call needle count -h and she'll tell you everything 🫶

Heads up bestie, this part is important: the options down below belong to the top-level parser only. That means you have to put them before the subcommand keyword. Everything you type after the subcommand keyword gets yeeted straight over to that subcommand's own sub-parser. Order matters, iykyk. 🔥

✨ OPTIONS ✨

🎀 Basic options:

  • -h, --help — prints the help page. Classic. Iconic. 🩷
  • -hh, --advanced-help — prints the help page including the advanced options, for when you're feeling like a main character who wants the full lore. 👑
  • --version — prints the version information. 🏷️
  • --copyright — prints the copyright/license information. Legal queen. ⚖️
  • --export-help (std::string) — exports the help page information. The value you pass must be one of [html, man] — anything else and she's not having it. 📤

🧚 VERSION 🧚

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

🔗 URL 🔗

https://github.com/seqan/needle

Go give her a star, she deserves it. ⭐

  • needle Copyright: BSD 3-Clause License
  • Author: Mitra Darvish
  • SeqAn Copyright: 2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.

And listen, if you use this in your academic works, please cite her — she's not asking for much, she's asking for credit, and honestly? Fair.

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

For the full copyright and/or warranty information, hit up --copyright. 🫶

okay that's the whole page!! huge shoutout to needle 1.0.3, dated 2024-11-07 — she ate, she left no crumbs, and she's out. mwah 💖💅✨

📦 where this page comes from