RAPTOR(1)

💖 NAME 💖

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

okay so basically this is RAPTOR(1), bestie, and it's giving "I have a truly unhinged number of nucleotide sequences and I need to know which ones are in here" energy. no cap. 🦋

✨ OPTIONS ✨

🎀 Basic options 🎀

• -h, --help — prints the help page. that's it, that's the whole vibe 💅
• -hh, --advanced-help — prints the help page including the advanced options. the deluxe edition, the director's cut 👑
• --version — prints the version information. receipts, basically 🧾
• --copyright — prints the copyright/license information 🫶
• --export-help (std::string) — export the help page information. the value must be one of [html, man]. so like, pick a format bestie, those are the only two 💀
• --index (std::filesystem::path) — hand over a valid path to an index. this is the main character of the whole operation tbh 🌟
• --query (std::filesystem::path) — give it a path to the query file. heads up: the input file must exist and read permissions must be granted, no exceptions, the program will simply not be doing that 🙈
• --output (std::filesystem::path) — a path to the output. where the results go to live their best life 🎀
• --threads (unsigned 8 bit integer) — the number of threads to use. default is 1. value must be a positive integer. go ahead and give it more, she can handle it 🔥
• --cache-thresholds — stores the computed thresholds with a unique name next to the index. next search call with this option on, the stored thresholds get re-used. so like, she remembers. iconic behavior honestly ⭐

two files get stored:

• threshold_*.bin: depends on pattern, window, kmer/shape, errors, and tau.
• correction_*.bin: depends on pattern, window, kmer/shape, p_max, and fpr.

🌸 EXAMPLES 🌸

look at her go:

raptor search --error 2 --index raptor.index --query queries.fastq --output search.output

ate. no crumbs. 💅

⭐ 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 click it, iykyk 🌈

👑 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.

okay bestie that's the whole page, you're officially educated 💖 this was raptor 2.0.1 (that long 74f815358db47... commit situation) from 2021-08-20--no-git, aka RAPTOR(1), and she's literally built different. mwah, go query something huge 🧚✨🌸