| RAPTOR(1) | RAPTOR(1) |
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 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].
- --parts (unsigned 8 bit integer)
- Splits the index in this many parts. Default: 1. Value must be a power of two.
- --kmer (unsigned 8 bit integer)
- The k-mer size. Default: 20. Value must be in range [1,32].
- --window (raptor::window)
- The window size. Default: k-mer size. Value must be a positive integer.
- --output (std::filesystem::path)
- Provide an output filepath or an output directory if --compute-minimiser is used.
- --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.
- --compute-minimiser
- Computes minimisers using cutoffs from Mantis (Pandey et al.). Does not create the index.
- --disable-cutoffs
- Do not apply cutoffs when using --compute-minimiser.
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¶
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) |