RAPTOR

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.