RAPTOR-PREPARE(1)

💖 RAPTOR-PREPARE — ok bestie, we're pre-filtering nucleotides today 💖

This is the manual page for raptor-prepare, section 1. Pull up a chair, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

Raptor-prepare — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. She's giving speed, she's giving efficiency, she's giving "your RAM could never" 💅

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🦋 SYNOPSIS 🦋

raptor prepare --input <file> --output <directory> [--threads <number>]
[--quiet] [--kmer <number>|--shape <01-pattern>] [--window <number>]
[--kmer-count-cutoff <number>|--use-filesize-dependent-cutoff]

Those brackets? Optional. That vertical bar? Pick one, not both — no cap. 🔥

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🌸 DESCRIPTION 🌸

So here's the tea: raptor prepare computes minimisers for use with raptor layout and raptor build. That's the whole job. She's the prep girlie so the other raptor commands can eat later. 👑

And the best part? If you crash 💀 — or you just wanna run it in pieces — she can continue where she left off. In multiple runs, even. Resilient queen energy, honestly.

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🎀 OPTIONS 🎀

💖 General options 💖

• --input (std::filesystem::path) — The file that contains your file names. Real talk: this file must hold at least one file path per line, and if a line has multiple paths they're separated by a whitespace. Each line = one bin. Now, valid extensions for those paths: [minimiser] if you're using preprocessed input from raptor prepare, or [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], and that list may be followed by [bz2,gz,bgzf]. The input file has to exist and you must have read permissions. No permissions, no minimisers, periodt. 🚫
• --output (std::filesystem::path) — A valid path for the output directory. ✨

She will create a minimiser.list inside the output directory. What's in it? A list of the generated minimiser files, in the same order as the input. Keeping it tidy, keeping it ordered, we love her.

⚠️ MAJOR heads up bestie: when you manually delete a .in_progress file, you also have to delete the matching .header and .minimiser file! Do not leave those orphans hanging, it's giving chaos 😭

Here's every output file she creates for each file:

• *.header: Contains the shape, window size, cutoff and minimiser count.
• *.minimiser: Contains binary minimiser values, one minimiser per line.
• *.in_progress: Temporary file to track process. Deleted after finishing computation.

• --threads (unsigned 8 bit integer) — How many threads you wanna throw at it. Default: 1. Value must be a positive integer. Go wild, but not too wild 🏃‍♀️
• --quiet — Do not print time and memory usage. For the girlies who don't wanna see the stats, just the results 🤫

🌈 k-mer options 🌈

• --kmer (unsigned 8 bit integer) — The k-mer size. Default: 20. Value must be in range [1,32]. Stay in your lane, range-wise. 🧚
• --window (unsigned 32 bit integer) — The window size. Default: k-mer size. Value must be a positive integer.
• --shape (std::string) — The shape to use for k-mers. Mutually exclusive with --kmer — pick a struggle, you can't have both. Parsed from right to left, which is lowkey iconic. Default: 11111111111111111111 (that's a k-mer of size 20). Value must match the pattern '[01]+'. Yes, literally just zeroes and ones. Binary baddie. 💅

🫶 Processing options 🫶

• --kmer-count-cutoff (unsigned 8 bit integer) — Only store k-mers with at least (>=) x occurrences. Mutually exclusive with --use-filesize-dependent-cutoff. Default: 1. Value must be in range [1,254].
• --use-filesize-dependent-cutoff — Apply cutoffs from Mantis(Pandey et al., 2018). Mutually exclusive with --kmer-count-cutoff. Again — one or the other, bestie 🙈

⭐ Common options ⭐

• -h, --help — Prints the help page.
• -hh, --advanced-help — Prints the help page including advanced options. The deluxe edition ✨
• --version — Prints the version information.
• --copyright — Prints the copyright/license information.
• --export-help (std::string) — Export the help page information. Value must be one of [html, man, ctd, cwl].

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🔥 EXAMPLES 🔥

k-mer and window, the classic combo:

raptor prepare --input bins.list --output some_directory --kmer 20 --window 24

Wanna cut off the low-count k-mers?

raptor prepare --input bins.list --output some_directory --kmer-count-cutoff 2

Or let the file size decide for you, main character style:

raptor prepare --input bins.list --output some_directory --use-filesize-dependent-cutoff

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💜 VERSION 💜

• Last update: Unavailable
• Raptor-prepare version: 3.0.1 (commit unavailable)
• Sharg version: 1.1.1
• SeqAn version: 3.4.0

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🌐 URL 🌐

https://github.com/seqan/raptor — go follow, go star, go say hi 🫶

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👑 LEGAL 👑

• Raptor-prepare Copyright: BSD 3-Clause License
• Author: Enrico Seiler
• Contact: enrico.seiler@fu-berlin.de
• SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.

And listen — if you're using this in your academic works, please cite:

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782

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

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And that's the whole page, bestie 🎀 this is raptor-prepare version 3.0.1 (commit u... Unavailable, from the RAPTOR-PREPARE(1) manual — last update info says Unavailable, so don't come for me about dates. Now go forth and minimise 💖✨