NAME

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

SYNOPSIS

       raptor search --index <file> --query <file> --output <file> [--threads <number>] [--quiet]
       [--error <number>|--threshold <number>] [--query_length <number>] [--tau <number>] [--pmax
       <number>] [--cache-thresholds]

DESCRIPTION

       Queries a Raptor index.

OPTIONS

   General options
       --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.        Valid        file        extensions       are
              [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly  followed
              by [bz2,gz,bgzf].

       --output (std::filesystem::path)
               A valid path for the output file. Write permissions must be granted.

       --threads (unsigned 8 bit integer)
              The number of threads to use. Default: 1. Value must be a positive integer.

       --quiet
              Do not print time and memory usage.

   Threshold method options
       If no option is set, --error 0 will be used as default.
       Setting  --query_length also skips validations associated with the query length, e.g., too
       long/short queries or a high variance in the query  lengths.  Notably,  queries  that  are
       shorter than the window size result in undefined behavior.

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

       --threshold (double)
              Ratio of k-mers that need to be found for a hit to occur. Mutually  exclusive  with
              --error. Default: None. Value must be in range [0,1].

       --query_length (unsigned 64 bit integer)
              The  query  length.  Only  influences  the  threshold  when  using --error. Enables
              skipping of the query length computation for both --error and --threshold. Default:
              Median of sequence lengths in query file.

   Dynamic thresholding options
       These option have no effect when using --threshold or k-mer size == window size.
       A  higher threshold means that less, in the extreme case even false negative, results will
       be produced.
       A lower threshold means that more, possibly false positive, results will be produced.

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

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

       --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 query_length, window, kmer/shape, errors, and tau.

       correction_*.bin: Depends on query_length, window, kmer/shape, p_max, and fpr.

   Common 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, ctd, cwl].

EXAMPLES

       raptor search --index raptor.index --query queries.fastq --output search.output

       raptor  search  --index  raptor.index   --query   queries.fastq   --output   search.output
       --threshold 0.7

       raptor search --index raptor.index --query queries.fastq --output search.output --error 2

       raptor  search --index raptor.index --query queries.fastq --output search.output --error 2
       --query_length 250

VERSION

       Last update: Unavailable
       Raptor-search version: 3.0.1 (commit unavailable)
       Sharg version: 1.1.1
       SeqAn version: 3.3.0-rc.2

URL

       https://github.com/seqan/raptor

LEGAL

       Raptor-search Copyright: BSD 3-Clause License
       Author: Enrico Seiler
       Contact: enrico.seiler@fu-berlin.de
       SeqAn Copyright: 2006-2023 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.