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: 3.4.0-rc.3

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.

raptor-search 3.0.1 (commit unavailable)           Unavailable                                  RAPTOR-SEARCH(1)