NAME

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

SYNOPSIS

       raptor build  --input  <file>  --output  <file>  [--threads  <number>]  [--quiet]  [--kmer
       <number>|--shape  <01-pattern>]  [--window  <number>]  [--fpr  <number>] [--hash <number>]
       [--parts <number>] [--compressed]

DESCRIPTION

       Constructs a Raptor index.

       The input may be a layout file from raptor layout, a list of minimiser files produced from
       raptor prepare, or a file with a list of files to process.

OPTIONS

   General options
       --input (std::filesystem::path)
              A  layout  file  from raptor layout, or a 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 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.

   k-mer options
       --kmer (unsigned 8 bit integer)
              The  k-mer  size.  Default:  20,  or  read from layout file. 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), or read from layout file.
              Value must match the pattern '[01]+'.

   Index options
       --fpr (double)
              The false positive rate. Default: 0.050000, or read from layout file. Value must be
              in range [0.000000,1.000000].

       --hash (unsigned 64 bit integer)
              The  number  of  hash functions to use. Default: 2, or read from layout file. Value
              must be in range [1,5].

       --parts (unsigned 8 bit integer)
              Splits the index in this many parts. Not available for the HIBF. Default: 1.  Value
              must be a power of two.

       --compressed
              Build a compressed index.

   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 build --input bins.list --kmer 19 --window 23 --fpr 0.05 --output raptor.index

       raptor build --input bins.list --shape 11011 --window 8 --output raptor.index

       raptor  build  --input  bins.list  --kmer  32  --window  32  --hash  3  --parts 4 --output
       raptor.index

       raptor build --input minimiser.list --fpr 0.05 --output raptor.index

       raptor build --input raptor.layout --output raptor.index

       raptor build --input raptor.layout --fpr 0.05 --output raptor.index

VERSION

       Last update: Unavailable
       Raptor-build 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-build 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.