RAPTOR-SEARCH(1)

💖 NAME 💖

raptor-search — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. no cap, it's the girlboss of huge nucleotide collections, and this is her manual page (RAPTOR-SEARCH(1), iykyk) 💅

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🌸 SYNOPSIS 🌸

raptor search --index <file> --query <file> --output <file> [--threads
<number>] [--quiet] [--error <number>|--threshold <number>]
[--query_length <number>] [--tau <number>] [--pmax <number>] [--cache-
thresholds]

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👑 DESCRIPTION 👑

okay so basically: it queries a Raptor index. that's the whole vibe. 🦋

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✨ OPTIONS ✨

🎀 General options

• --index (std::filesystem::path) — give it a valid path to an index. Parts: without the _0 suffix, bestie, don't forget that part 🫶
• --query (std::filesystem::path) — hand over a path to the query file. the input file has to actually exist and read permissions must be granted, or she's not answering. valid file extensions are [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf] ✨
• --output (std::filesystem::path) — a valid path for the output file. write permissions must be granted. yes ma'am 🎀
• --threads (unsigned 8 bit integer) — how many threads to use. Default: 1. the value must be a positive integer. more threads = more girlies helping out 💅
• --quiet — do not print time and memory usage. she's silent, she's mysterious 💀

🧚 Threshold method options

if no option is set, --error 0 will be used as default. periodt.

setting --query_length also skips validations associated with the query length, e.g. too long/short queries or a high variance in the query lengths. and notably: queries that are shorter than the window size result in undefined behavior. bestie please, do not do that 😭

• --error (unsigned 8 bit integer) — the number of errors. mutually exclusive with --threshold. Default: 0. the value must be a positive integer or 0.
• --threshold (double) — the ratio of k-mers that need to be found for a hit to occur. mutually exclusive with --error. Default: None. value must be in range [0,1].
• --query_length (unsigned 64 bit integer) — the query length. it only influences the threshold when using --error. it also enables skipping of the query length computation for both --error and --threshold. Default: median of sequence lengths in query file. queen of efficiency 👑

🌈 Dynamic thresholding options

these options have no effect when using --threshold or when k-mer size == window size. so like, don't come for them, they're off the clock 💤

a higher threshold means that less, in the extreme case even false negative, results will be produced. a lower threshold means that more, possibly false positive, results will be produced.

• --tau (double) — the higher tau, the lower the threshold. Default: 0.9999. value must be in range [0,1].
• --p_max (double) — the higher p_max, the lower the threshold. Default: 0.15. value must be in range [0,1].
• --cache-thresholds — stores the computed thresholds with a unique name next to the index. in the next search call using this option, the stored thresholds are re-used. two files get stored:
  • threshold_*.bin: depends on query_length, window, kmer/shape, errors, and tau.
  • correction_*.bin: depends on query_length, window, kmer/shape, p_max, and fpr.

💜 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 🍓

here's the group chat receipts, fr fr:

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

raptor search --index raptor.index --query queries.fastq --output search.output --threshold 0.7

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

raptor search --index raptor.index --query queries.fastq --output search.output --error 2 --query_length 250

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⭐ VERSION ⭐

• Last update: Unavailable
• Raptor-search 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 say hi 🫶

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📜 LEGAL 📜

• Raptor-search 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.
• 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.

cite her in your papers or she WILL know 👀

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and that's a wrap, bestie 💖 this was raptor-search version 3.0.1 (commit un... Unavailable), last updated Unavailable — literally unavailable, iconic of her. catch you in the next RAPTOR-SEARCH(1) 💅✨