RAPTOR(1)

💖 RAPTOR 💖

okay bestie, so this is the manual page for raptor, and she's that girl. RAPTOR(1) is the vibe, raptor is the command, and by the end of this you're gonna be filtering nucleotide sequences like it's nothing. no cap. 🦋

---

✨ NAME ✨

Raptor — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

like… literally what it says. she pre-filters. she's fast. she's space-efficient. she's giving main character energy for your very large collections of nucleotide sequences. 👑

---

🎀 POSITIONAL ARGUMENTS 🎀

• ARGUMENT-1 (std::filesystem::path) — the file containing color and file names. bestie, this file has to have at least one file path per line, and if there's more than one path on a line, separate them with whitespace. every single line in that file = one bin. 💅

valid extensions for the paths inside that file are [minimiser] when you're preprocessing, and [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam] otherwise — possibly followed by [bz2,gz,bgzf].

🌸 the input file must exist and read permissions must be granted. no file, no permissions, no party. that's the rules.

---

✨ OPTIONS ✨

🫶 Basic options:

• -h, --help — prints the help page. classic. iconic. helpful.
• -hh, --advanced-help — prints the help page including the advanced options. it's giving ✨ director's cut ✨.
• --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].
• --kmer (unsigned 8 bit integer) — the k-mer size. default: 20. value must be in range [1,32].
• --output (std::filesystem::path) — provide an output filepath.
• --size (std::string) — the size in bytes of the resulting index. default: 1k. must be an integer followed by [k,m,g,t] (case insensitive).
• --hash (unsigned 64 bit integer) — the number of hash functions to use. default: 2. value must be in range [1,5].
• --threads (unsigned 8 bit integer) — the numer of threads to use. default: 1. value must be a positive integer. (yes bestie, the original says "numer" — we're keeping it, that's canon 💀)
• --compressed — build a compressed index.

---

🌈 EXAMPLES 🌈

okay so here's how the girlies actually run it:

raptor build --kmer 19 --window 23 --size 8m --output raptor.index all_bin_paths.txt

raptor build --kmer 19 --window 23 --compute-minimiser --output precomputed_minimisers all_bin_paths.txt

raptor build --size 8m --output minimiser_raptor.index all_minimiser_paths.txt

periodt. copy, paste, slay. 💅

---

🌟 VERSION 🌟

• Last update: 2021-08-20--no-git
• Raptor version: 2.0.1 (74f815358db47037e93a56b826a9df3692e55680--no-git)
• Sharg version: 1.0.0
• SeqAn version: 3.2.0

---

🔗 URL 🔗

https://github.com/seqan/raptor

go follow her, she's iconic.

---

👑 LEGAL 👑

• Raptor Copyright: BSD 3-Clause License
• Author: Enrico Seiler
• Contact: enrico.seiler@fu-berlin.de
• SeqAn Copyright: 2006-2022 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
• 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.

---

aaaand that's the whole page, bestie 🎀 this was raptor 2.0.1 (74f815358db47..., dated 2021-08-20--no-git, and yeah she's RAPTOR(1) — go build an index, you absolute icon 💖✨🦋🌸💅