---
name: "raptor-search"
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-search"
---

# raptor-search(1)

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

## NAME

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

## SYNOPSIS

**raptor** search --index \<file\> --query \<file\> --output \<file\> \[--threads \<number\>\] \[--quiet\] \[--error \<number\>\|--threshold \<number\>\] \[--query\_length \<number\>\] \[--tau \<number\>\] \[--pmax \<number\>\] \[--cache-thresholds\]

## DESCRIPTION

Queries a Raptor index.

## OPTIONS

### General options

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

  Provide a valid path to an index. Parts: Without suffix \_0

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

  Provide a path to the query file. The input file must exist and read permissions must be granted. Valid file extensions are \[embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam\], possibly followed by \[bz2,gz,bgzf\].

- **--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.

### Threshold method options

**If no option is set, --error 0 will be used as default.**\
 Setting --query\_length also skips validations associated with the query length, e.g., too long/short queries or a high variance in the query lengths. Notably, queries that are shorter than the window size result in undefined behavior.

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

  The number of errors. Mutually exclusive with --threshold. Default: 0. Value must be a positive integer or 0.

- **--threshold** (*double*)

  Ratio of k-mers that need to be found for a hit to occur. Mutually exclusive with --error. Default: None. Value must be in range \[0,1\].

- **--query\_length** (*unsigned 64 bit integer*)

  The query length. Only influences the threshold when using --error. Enables skipping of the query length computation for both --error and --threshold. Default: Median of sequence lengths in query file.

### Dynamic thresholding options

**These option have no effect when using --threshold or k-mer size == window size.**\
 A higher threshold means that less, in the extreme case even false negative, results will be produced.\
 A lower threshold means that more, possibly false positive, results will be produced.

- **--tau** (*double*)

  The higher tau, the lower the threshold. Default: 0.9999. Value must be in range \[0,1\].

- **--p\_max** (*double*)

  The higher p\_max, the lower the threshold. Default: 0.15. Value must be in range \[0,1\].

- **--cache-thresholds**

  Stores the computed thresholds with an unique name next to the index. In the next search call using this option, the stored thresholds are re-used. Two files are stored:

- **threshold\_\*.bin**: Depends on query\_length, window, kmer/shape, errors, and tau.

  - **correction\_\*.bin**: Depends on query\_length, window, kmer/shape, p\_max, and fpr.

  ### 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 search --index raptor.index --query queries.fastq --output search.output

raptor search --index raptor.index --query queries.fastq --output search.output --threshold 0.7

raptor search --index raptor.index --query queries.fastq --output search.output --error 2

raptor search --index raptor.index --query queries.fastq --output search.output --error 2 --query\_length 250

## VERSION

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