RAPTOR(1)

📦
version 3.0.1 · 4 versions
, in ubuntu resolute, ubuntu stonking

💖 RAPTOR — bestie's guide to the pre-filter 💖

okay so real talk, Raptor is a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences ✨

🌸 NAME 🌸

Raptor — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. that's the whole name bestie, it's giving "short and iconic" 💅

🦋 DESCRIPTION 🦋

Raptor is a whole system for approximately searching so many queries — think next-generation sequencing reads, think transcripts — against huge collections of nucleotide sequences 🌈

how does it do it without dying, you ask? bestie, it uses:

  • winnowing minimizers to define a set of representative k-mers 🎀
  • an extension of the interleaved Bloom filters (IBFs) as a set membership data structure
  • probabilistic thresholding for minimizers

and the way our approach lets you compress and partition the IBF so secondary memory can actually get used effectively... yeah, that's the slay. no cap, that's the whole point. 👑

🫶 SUBCOMMANDS 🫶

you literally cannot just run this program raw. it must be invoked with one of the following subcommands:

  • build
  • layout
  • prepare
  • search
  • upgrade

see the respective help page for the details, like fr fr just call something like Raptor build -h and it'll tell you 🧚

heads up bestie 💀 the options below belong to the top-level parser and have to be specified before the subcommand key word. every argument after the subcommand key word gets passed on to the corresponding sub-parser. order matters, iykyk.

✨ OPTIONS ✨

🌟 Common options 🌟

  • -h, --help — prints the help page. the classic. the goat.
  • -hh, --advanced-help — prints the help page including advanced options 🔥 the deluxe version
  • --version — prints the version information 🎀
  • --copyright — prints the copyright/license information 👑
  • --export-help (std::string) — export the help page information. the value must be one of [html, man, ctd, cwl] 😭 pick one, choose your fighter

💜 VERSION 💜

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

🌈 URL 🌈

https://github.com/seqan/raptor

go give it a star bestie, it's the least you could do 💖

  • Raptor 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. periodt. ⭐

and that's the whole page bestie 🥰 no notes. this was raptor 3.0.1 (commit unavailable), dated Unavailable, and it's chilling in section RAPTOR(1) — mwah, go read some sequences 💜🌸🦋

📦 where this page comes from