---
name: "raptor-build"
section: "1"
platform: "linux"
package: "seqan-raptor"
version: "3.0.1+ds-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/raptor-build"
---

# raptor-build(1)

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

## NAME

Raptor-build - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

## SYNOPSIS

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

## DESCRIPTION

Constructs a Raptor index.

The input may be a layout file from **raptor layout**, a list of minimiser files produced from **raptor prepare**, or 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.

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

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

- **--quiet**

  Do not print time and memory usage.

### 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 '\[01\]+'.

### Index options

- **--fpr** (*double*)

  The false positive rate. Default: 0.050000, or read from layout file. Value must be in range \[0.000000,1.000000\].

- **--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.

- **--compressed**

  Build a compressed index.

### 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 \[html, man, ctd, cwl\].

## EXAMPLES

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

## VERSION

**Last update:** Unavailable\
 **Raptor-build version:** 3.0.1 (commit unavailable)\
 **Sharg version:** 1.1.1\
 **SeqAn version:** 3.4.0-rc.3

## URL

https://github.com/seqan/raptor

## 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**.