RAPTOR-BUILD(1)

💖 RAPTOR-BUILD(1) 💖

okay bestie, sit down, hydrate, because we're about to talk about raptor-build and honestly? it's giving iconic. this is the raptor-build(1) manual page and i'm gonna walk you through every single thing in it, no skips, no "we'll come back to that", periodt. 🦋

---

✨ NAME ✨

Raptor-build — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. literally so fast. so space-efficient. so much nucleotide. 💅

---

✨ SYNOPSIS ✨

raptor build --input <file> --output <file> [--threads <number>]
[--quiet] [--kmer <number>|--shape <01-pattern>] [--window <number>]
[--fpr <number>] [--hash <number>] [--parts <number>] [--compressed]

that's the whole vibe. --input and --output are the only mandatory besties, everything else is optional glitter. ✨

---

✨ DESCRIPTION ✨

it constructs a Raptor index. that's the job. that's what it does. 👑

and the input? it can be any of these three things, no cap:

• a layout file from raptor layout 🎀
• a list of minimiser files produced from raptor prepare 🧚
• a file with a list of files to process 🌸

---

✨ OPTIONS ✨

💖 General options

• --input (std::filesystem::path) — a layout file from raptor layout, or a file containing file names. the file must contain at least one file path per line, with multiple paths being separated by a whitespace. each line in the file corresponds to one bin. valid extensions for the paths in the file are [minimiser] when using preprocessed input from raptor prepare, and [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf]. the input file must exist and read permissions must be granted. 🫶
• --output (std::filesystem::path) — a valid path for the output file. write permissions must be granted. no write permission, no index, sorry babe 🚫
• --threads (unsigned 8 bit integer) — the number of threads to use. default: 1. value must be a positive integer. more threads = more main character energy ⚡
• --quiet — do not print time and memory usage. she's mysterious. she's silent. 🙈

🌸 k-mer options

• --kmer (unsigned 8 bit integer) — the k-mer size. default: 20, or read from layout file. value must be in range [1,32]. ✨
• --window (unsigned 32 bit integer) — the window size. default: k-mer size. value must be a positive integer. 🪟
• --shape (std::string) — the shape to use for k-mers. mutually exclusive with --kmer. parsed from right to left. default: 11111111111111111111 (a k-mer of size 20), or read from layout file. value must match the pattern '[01]+'. it's giving binary couture 🎀

🔥 Index options

• --fpr (double) — the false positive rate. default: 0.050000, or read from layout file. value must be in range [0.000000,1.000000]. how often do we lie? not often. 🫣
• --hash (unsigned 64 bit integer) — the number of hash functions to use. default: 2, or read from layout file. value must be in range [1,5]. 🍓
• --parts (unsigned 8 bit integer) — splits the index in this many parts. not available for the HIBF. default: 1. value must be a power of two. 2, 4, 8, 16… you get it 💅
• --compressed — build a compressed index. zip it, squeeze it, slay it. 🗜️✨

👑 Common options

• -h, --help — prints the help page. your little map 🗺️
• -hh, --advanced-help — prints the help page including advanced options. the director's cut 🎬
• --version — prints the version information. 🏷️
• --copyright — prints the copyright/license information. read it, respect it 📜
• --export-help (std::string) — export the help page information. value must be one of [html, man, ctd, cwl]. 🌈

---

✨ EXAMPLES ✨

bestie these are verbatim, do not touch, do not remix, just copy:

raptor build --input bins.list --kmer 19 --window 23 --fpr 0.05 --output
raptor.index

raptor build --input bins.list --shape 11011 --window 8 --output
raptor.index

raptor build --input bins.list --kmer 32 --window 32 --hash 3 --parts 4
--output raptor.index

raptor build --input minimiser.list --fpr 0.05 --output raptor.index

raptor build --input raptor.layout --output raptor.index

raptor build --input raptor.layout --fpr 0.05 --output raptor.index

see how the last two don't even need k-mer stuff? the layout file already knows. she's self-sufficient. 💅

---

✨ VERSION ✨

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

---

✨ URL ✨

https://github.com/seqan/raptor

go look, it's free, it's open source, it's iconic 🔗

---

✨ LEGAL ✨

• Raptor-build 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. fr fr, go read it, it's right there 🌸

---

okay that's the whole page, you ate it, you understood it, i'm so proud 🥹 this was raptor-build version 3.0.1 (commit una... Unavailable), last updated Unavailable — so whenever you're reading this, that's when it's from 💀✨ byeee, go build an index bestie 💖🦋🎀