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. Parts: Without suffix _0

       --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.

       --error (unsigned 8 bit integer)
              The number of errors Default: 0. Value must be a positive integer or 0.

       --tau (double)
              Used in the dynamic thresholding. The higher tau, the lower the threshold. Default:
              0.9999. Value must be in range [0,1].

       --threshold (double)
              If set, this threshold is used instead of the probabilistic models.  Default:  nan.
              Value must be in range [0,1].

       --p_max (double)
              Used  in  the  dynamic  thresholding.  The  higher  p_max, the lower the threshold.
              Default: 0.15. Value must be in range [0,1].

       --fpr (double)
              The false positive rate used for building the index. Default: 0.05. Value  must  be
              in range [0,1].

       --pattern (raptor::pattern_size)
              The pattern size. Default: Median of sequence lengths in query file.

       --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)