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: 3.4.0-rc.3

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.

raptor-prepare 3.0.1 (commit unavailable)          Unavailable                                 RAPTOR-PREPARE(1)