---
name: "raptor-prepare"
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-prepare"
---

# raptor-prepare(1)

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

## NAME

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

## SYNOPSIS

**raptor** prepare --input \<file\> --output \<directory\> \[--threads \<number\>\] \[--quiet\] \[--kmer \<number\>\|--shape \<01-pattern\>\] \[--window \<number\>\] \[--kmer-count-cutoff \<number\>\|--use-filesize-dependent-cutoff\]

## DESCRIPTION

Computes minimisers for the use with **raptor layout** and **raptor build**.

Can continue where it left off after a crash or in multiple runs.

## OPTIONS

### General options

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

  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 directory.

- Will create a **minimiser.list** inside the output directory. This file contains a list of generated minimiser files, in the same order as the input.

  - **When you manually delete a .in\_progress file, also delete the corresponding .header and .minimiser file!**

  - Created output files for each file:

  - **\*.header**: Contains the shape, window size, cutoff and minimiser count.

  - **\*.minimiser**: Contains binary minimiser values, one minimiser per line.

  - **\*.in\_progress**: Temporary file to track process. Deleted after finishing computation.

  - **--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. 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). Value must match the pattern '\[01\]+'.

### Processing options

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

  Only store k-mers with at least (\>=) x occurrences. Mutually exclusive with --use-filesize-dependent-cutoff. Default: 1. Value must be in range \[1,254\].

- **--use-filesize-dependent-cutoff**

  Apply cutoffs from Mantis(Pandey et al., 2018). Mutually exclusive with --kmer-count-cutoff.

### 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 prepare --input bins.list --output some\_directory --kmer 20 --window 24

raptor prepare --input bins.list --output some\_directory --kmer-count-cutoff 2

raptor prepare --input bins.list --output some\_directory --use-filesize-dependent-cutoff

## VERSION

**Last update:** Unavailable\
 **Raptor-prepare 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-prepare 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**.