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RAPTOR(1) RAPTOR(1)

NAME

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

POSITIONAL ARGUMENTS

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:

Prints the help page.
Prints the help page including advanced options.
Prints the version information.
Prints the copyright/license information.
Export the help page information. Value must be one of [html, man].
The k-mer size. Default: 20. Value must be in range [1,32].
Provide an output filepath.
The size in bytes of the resulting index. Default: 1k. Must be an integer followed by [k,m,g,t] (case insensitive).
The number of hash functions to use. Default: 2. Value must be in range [1,5].
The numer of threads to use. Default: 1. Value must be a positive integer.
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.

2021-08-20--no-git raptor 2.0.1 (74f815358db47037e93a56b826a9df3692e55680--no-git)