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 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].

       --parts (unsigned 8 bit integer)
              Splits the index in this many parts. Default: 1. Value must be a power of two.

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

       --window (raptor::window)
              The window size. Default: k-mer size. Value must be a positive integer.

       --output (std::filesystem::path)
              Provide an output filepath or an output directory if --compute-minimiser is used.

       --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.

       --compute-minimiser
              Computes  minimisers using cutoffs from Mantis (Pandey et al.). Does not create the
              index.

       --disable-cutoffs
              Do not apply cutoffs when using --compute-minimiser.

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)