NEEDLE-COUNT(1)

💖 NEEDLE-COUNT(1) — the iconic little expression estimator 💖

okay bestie, sit down, hydrate, because we're about to talk about needle-count — it grabs an expression value depending on minimizers. it's like a whole alternative to pseudoaligners like kallisto, no cap. it estimates the expression value for all the sequences in the genome file, based on the exact minimiser occurrences of the sequence files you hand it. 🦋

⚠️ real talk for one sec: please run genome beforehand to create the genome file. the genome file does not manifest itself out of vibes. it's giving prerequisite. 😭

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🌸 POSITIONAL ARGUMENTS 🌸

• ARGUMENT-1 (List of std::filesystem::path) — bestie, please provide at least one sequence file. at least one. one is the minimum. Default: [].

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✨ OPTIONS ✨

🎀 Basic options 🎀

• -h, --help — prints the help page. that's it, that's the whole job. 💅
• -hh, --advanced-help — prints the help page including the advanced options. the deluxe edition. the director's cut. 👑
• --version — prints the version information.
• --copyright — prints the copyright/license information. the receipts, basically.
• --export-help (std::string) — exports the help page information. the value has to be one of [html, man] — those two, nobody else invited. 🌈
• -k, --kmer (unsigned 8 bit integer) — defines the k-mer size for the minimisers. Default: 20. Default: 20. (yes babe it really says it twice, I'm not editing the source, both defaults are staying, periodt 💀)
• -w, --window (unsigned 32 bit integer) — defines the window size for the minimisers. Default: 60. Default: 0. (two defaults, both canon, I don't make the rules 🫶)
• --shape (unsigned 64 bit integer) — defines a shape for the minimisers using the decimal of a bitvector, where 0 means that position is ignored and 1 means that position is considered. Default: ungapped. Default: 0. 🌸
• --seed (unsigned 64 bit integer) — defines the seed for the minimisers. Default: 0.
• -o, --out (std::filesystem::path) — the directory where output files should be saved. Default: "./".
• -t, --threads (unsigned 8 bit integer) — number of threads to use. Default: 1. Default: 1. (twins 💖)
• --include (std::filesystem::path) — please provide one sequence file with transcripts.
• --genome (std::filesystem::path) — please provide one *.genome file created with the genome command. Default: "".
• -p, --paired — if set, experiments are paired. Default: Not paired. 🔥

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⭐ VERSION ⭐

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

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🌈 URL 🌈

https://github.com/seqan/needle

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👑 LEGAL 👑

• needle-count 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

for full copyright and/or warranty information see --copyright. 🫶

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okay that's the whole page, and if you want the vibe check on where this came from: this is needle-count, version 1.0.3, dated 2024-11-07 — that's the sauce and the source, bestie. go estimate some expression, you absolute main character. 🧚✨💜