lunar (1) raptor-socks-lookup-kmer.1.gz
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. raptor 2.0.1 (74f815358db47037e93a56b8262021-08-20--no-git-git) RAPTOR(1)