---
name: "raptor-socks-lookup-kmer"
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-lookup-kmer"
---

# raptor-socks-lookup-kmer(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.

## 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 \[html, man\].

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

  Provide a valid path to an index.

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

  Provide a path to the query file. The input file must exist and read permissions must be granted.

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

  Provide a path to the output.

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

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

- **--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 pattern, window, kmer/shape, errors, and tau. **correction\_\*.bin**: Depends on pattern, window, kmer/shape, p\_max, and fpr.

## EXAMPLES

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

## 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**.