RAPTOR-LAYOUT(1)

🦋 RAPTOR-LAYOUT(1) — the manual page, but make it make sense

okay bestie, so this is the raptor-layout page from the RAPTOR-LAYOUT(1) manual and I'm about to explain it to you like we're texting at 1am. buckle up 💖

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✨ NAME ✨

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

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🌸 DESCRIPTION 🌸

So what it does is compute an HIBF layout that tries to minimize the disk space consumption of the resulting index. The space gets estimated using a k-mer count per user bin, and that count represents the potential density — yes the manpage literally wrote "denisity", we love a typo moment, no notes 💀 — in a technical bin inside an interleaved Bloom filter.

Then you take the resulting layout and pass it to raptor (https://github.com/seqan/raptor) to build the index and run queries. that's the whole vibe. 🫶

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👑 OPTIONS 👑

💅 Main options:

• --input-file (std::filesystem::path) — your input has to be a file full of paths to sequence data you want to estimate, and it's one filepath per line. If your file also carries auxiliary info like species IDs, then bestie your file must be tab-separated. no cap.

Example file:

/absolute/path/to/file1.fasta

/absolute/path/to/file2.fa.gz

• --kmer-size (unsigned 8 bit integer) — the k-mer size influences how the input gets size-estimated. Pick one that's too small and your files will look more similar than they actually are (fake friendship 😭). Pick one that's too large and you might miss out on certain similarities. For DNA sequences, a k-mer size between [16,32] has proven to work well. Default: 19.
• --num-hash-functions (unsigned 64 bit integer) — how many hash functions to use when building the HIBF from the resulting layout. This parameter is needed so the index size gets estimated correctly while the layout is being computed. Default: 2.
• --false-positive-rate (double) — the false positive rate you're aiming for when you build the HIBF from the resulting layout. Also needed to correctly estimate the index size while computing the layout. Default: 0.05.
• --output-filename (std::filesystem::path) — a file name for the resulting layout. Default: "binning.out".
• --threads (unsigned 64 bit integer) — the number of threads to use. Currently only the merging of sketches is parallelized, so if the flag --disable-rearrangement is set, --threads will have no effect. Default: 1. Value must be in range [1,18446744073709551615].

🎀 HyperLogLog Sketches:

To improve the layout, you can estimate the sequence similarities using HyperLogLog sketches. it's giving smart 💅

• --disable-estimate-union — the sketches are used to estimate the sequence similarity among a set of user bins. This improves the layout computation, because merging user bins that don't increase technical bin sizes gets preferred. It may use more RAM, so you can turn it off in RAM-critical environments. Attention: this also disables rearrangement, which depends on union estimations. ⚠️
• --disable-rearrangement — as a preprocessing step, rearranging the order of the given user bins based on their sequence similarity may lead to favourable small unions and therefore a smaller index. Depending on the number of input samples (user bins), this can be time-consuming, so you can disable it if a suboptimal layout is good enough for you. 🙈

Parameter Tweaking:

(this section is empty in the original — the manpage is giving placeholder energy, we respect it tho 💜)

Special options

(also empty. iconic. nothing to report bestie.)

📚 REFERENCES

• [1] Philippe Flajolet, Éric Fusy, Olivier Gandouet, Frédéric Meunier. HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm. AofA: Analysis of Algorithms, Jun 2007, Juan les Pins, France. pp.137-156. hal-00406166v2, https://doi.org/10.46298/dmtcs.3545

🧚 Common options

• -h, --help — Prints the help page.
• -hh, --advanced-help — Prints the help page including advanced options.
• --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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⭐ VERSION

• Last update: Unavailable
• Raptor-layout 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

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💜 LEGAL

• Raptor-layout Copyright: BSD 3-Clause License
• Author: Svenja Mehringer
• Contact: svenja.mehringer@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.

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remade from <rainbow>raptor-layout 3.0.1 (commit un... Unavailable</rainbow> and the whole page was last updated <purple>Unavailable</purple> — so yeah, the version info is doing its little mystery era, and this whole thing lives under the RAPTOR-LAYOUT(1) manual. periodt. 💅✨