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 color and 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].

       --kmer (unsigned 8 bit integer)
              The k-mer size. Default: 20. Value must be in range [1,32].

       --output (std::filesystem::path)
              Provide an output filepath.

       --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.

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

       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)