NEEDLE-IBF(1)

💖 NEEDLE-IBF(1) — bestie's guide to needle-ibf 💖

okay so. you opened the manual for needle-ibf, and I'm gonna hold your hand through every single flag, no skips, no cap. this thing constructs the Needle index. that's the whole vibe. let's go 💅

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✨ NAME ✨

needle-ibf — constructs the Needle index. yep. that's her. that's the job. 🫶

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🌸 POSITIONAL ARGUMENTS 🌸

• ARGUMENT-1 (List of std::filesystem::path) — okay so here's the tea ☕: you gotta hand over at least one sequence file. OR — plot twist — you can give one single file that contains all the sequence files, and that one file needs the extension .lst. that's the move. Default: []. (aka nothing, aka you must bring something, bestie 😭)

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👑 OPTIONS 👑

🎀 Basic options 🎀

• -h, --help — prints the help page. classic. iconic. 🎀
• -hh, --advanced-help — prints the help page but make it ✨extra✨ — this one includes the advanced options too. yes, double-h is real, we love her.
• --version — prints the version information. go on, ask her how old she is 💀
• --copyright — prints the copyright/license information. the ✨legal era✨.
• --export-help (std::string) — exports the help page info. the value must be one of [html, man]. that's it. those two. don't try to be creative 🙈
• -k, --kmer (unsigned 8 bit integer) — defines the k-mer size for the minimisers. Default: 20. Default: 20. (yes I said it twice, because the page says it twice, and honestly? she's worth repeating 💖)
• -w, --window (unsigned 32 bit integer) — defines the window size for the minimisers. Default: 60. Default: 0. (both listed, don't yell at me, that's literally what the page says 👀)
• --shape (unsigned 64 bit integer) — defines a shape for the minimisers by giving the decimal of a bitvector, where 0 means "position, ignore her" and 1 means "position, you're so 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. (again twice, again I report faithfully, again I love her 💅)
• -c, --compressed — if c is set, the IBFS are compressed. Default: Not compressed. 🗜️
• -f, --fpr (List of double) — a list of bin false positive rate per expression level. if only one is given, then that fpr gets used for all expression levels. one size fits all energy. Default: [].
• -e, --expression_thresholds (List of unsigned 16 bit integer) — which expression thresholds should be used for constructing the IBFs. Default: [].
• -l, --number_expression_thresholds (unsigned 8 bit integer) — number of expression thresholds. you can set this instead of expression_thresholds, and then the expression thresholds get determined automatically. she's like "don't worry abt it, I got this". Default: 0.
• -n, --hash (unsigned 64 bit integer) — number of hash functions to use when constructing one IBF. Default: 1.
• --include (std::filesystem::path) — a sequence file containing minimizers; only those minimizers will be considered. like a guest list. if you're not on it, you're not getting in 🚫 Default: "".
• --exclude (std::filesystem::path) — a sequence file containing minimizers that should not be stored. the block list, bestie. Default: "".
• --samples (List of signed 32 bit integer) — defines which samples belong together. important: the sum has to be equal to number of sequence files. math girlies rise 👑 Default: every sequence file is one sample from one experiment. Default: [].
• -p, --paired — if set, the experiments are paired. ship them 🫶 Default: Not paired.
• --cutoff (List of unsigned 8 bit integer) — defines, for each sample, what number of found minimisers should be considered the result of a sequencing error and therefore get ignored. it's giving "we don't talk about that one". Default: every sample has an automatically generated cutoff, which is based on the file size. Default: [].
• --experiment-names (bool) — if set, the names of the experiments are stored in a txt file. 📝 Default: 0.
• --levels-by-genome (std::filesystem::path) — a sequence file containing minimizers; only those minimizers will be considered for determining the expression thresholds. (same guest-list energy, different party 🎉) Default: "".
• --ram — if ram is set and multiple threads are used, the multithreading is more RAM friendly, at the cost of being slower. so: gentle on memory, slow on vibes. your call, bestie 😌

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🦋 VERSION 🦋

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

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🔥 URL 🔥

https://github.com/seqan/needle

go say hi. star the repo. it's the least you can do 💜

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💜 LEGAL 💜

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

📚 and listen — 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. (iconic flag behavior, honestly) ✨

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and that's the whole page, bestie!! 🌈 needle-ibf version 1.0.3, last updated 2024-11-07, and this whole manual is literally titled NEEDLE-IBF(1) — now go construct that index, main character 💅👑💖