---
name: "raptor-socks-build"
section: "1"
platform: "linux"
package: "seqan-raptor"
version: "2.0.0.0.git.fecfbca+ds-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/raptor-socks-build"
---

# raptor-socks-build(1)

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.

## POSITIONAL ARGUMENTS

- **ARGUMENT-1** (*std::filesystem::path*)

  File containing color and 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  preprocessing, and \[embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam\], possibly followed by \[bz2,gz,bgzf\] otherwise.  The input file must exist and read permissions must be granted.

## OPTIONS

### Basic 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 \[html, man\].

- **--kmer** (*unsigned 8 bit integer*)

  The k-mer size. Default: 20. Value must be in range \[1,32\].

- **--output** (*std::filesystem::path*)

  Provide an output filepath.

- **--size** (*std::string*)

  The size in bytes of the resulting index. Default: 1k. Must be an integer followed by \[k,m,g,t\] (case insensitive).

- **--hash** (*unsigned 64 bit integer*)

  The number of hash functions to use. Default: 2. Value must be in range \[1,5\].

- **--threads** (*unsigned 8 bit integer*)

  The numer of threads to use. Default: 1. Value must be a positive integer.

- **--compressed**

  Build a compressed index.

## EXAMPLES

raptor build --kmer 19 --window 23 --size 8m --output raptor.index all\_bin\_paths.txt

raptor build --kmer 19 --window 23 --compute-minimiser --output precomputed\_minimisers all\_bin\_paths.txt

raptor build --size 8m --output minimiser\_raptor.index all\_minimiser\_paths.txt

## 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

## 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**.