NAME

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

SYNOPSIS

       raptor prepare --input <file> --output <directory> [--threads <number>] [--quiet]  [--kmer
       <number>|--shape  <01-pattern>]  [--window  <number>] [--kmer-count-cutoff <number>|--use-
       filesize-dependent-cutoff]

DESCRIPTION

       Computes minimisers for the use with raptor layout and raptor build.

       Can continue where it left off after a crash or in multiple runs.

OPTIONS

   General options
       --input (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      using     preprocessed     input     from     raptor     prepare,     and
              [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly  followed
              by [bz2,gz,bgzf].  The input file must exist and read permissions must be granted.

       --output (std::filesystem::path)
               A valid path for the output directory.

       Will  create  a  minimiser.list  inside the output directory. This file contains a list of
       generated minimiser files, in the same order as the input.

       When you manually delete a .in_progress file, also delete the  corresponding  .header  and
       .minimiser file!

       Created output files for each file:

       *.header: Contains the shape, window size, cutoff and minimiser count.

       *.minimiser: Contains binary minimiser values, one minimiser per line.

       *.in_progress: Temporary file to track process. Deleted after finishing computation.

       --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.

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

       --window (unsigned 32 bit integer)
              The window size. Default: k-mer size. Value must be a positive integer.

       --shape (std::string)
              The  shape  to use for k-mers. Mutually exclusive with --kmer. Parsed from right to
              left. Default: 11111111111111111111 (a k-mer of size  20).  Value  must  match  the
              pattern '[01]+'.

   Processing options
       --kmer-count-cutoff (unsigned 8 bit integer)
              Only  store k-mers with at least (>=) x occurrences. Mutually exclusive with --use-
              filesize-dependent-cutoff. Default: 1. Value must be in range [1,254].

       --use-filesize-dependent-cutoff
              Apply cutoffs from Mantis(Pandey et al., 2018).  Mutually  exclusive  with  --kmer-
              count-cutoff.

   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 prepare --input bins.list --output some_directory --kmer 20 --window 24

       raptor prepare --input bins.list --output some_directory --kmer-count-cutoff 2

       raptor prepare --input bins.list --output some_directory --use-filesize-dependent-cutoff

VERSION

       Last update: Unavailable
       Raptor-prepare 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-prepare 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.