NAME

       needle-ibf - Constructs the Needle index.

POSITIONAL ARGUMENTS

       ARGUMENT-1 (List of std::filesystem::path)
              Please  provide  at  least  one  sequence  file  OR provide one file containing all
              sequence files with the extension '.lst'. Default: [].

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].

       -k, --kmer (unsigned 8 bit integer)
              Define k-mer size for the minimisers. Default: 20. Default: 20.

       -w, --window (unsigned 32 bit integer)
              Define window size for the minimisers. Default: 60. Default: 0.

       --shape (unsigned 64 bit integer)
              Define a shape for the minimisers by the decimal of a bitvector, where 0 symbolizes
              a position to be ignored, 1 a position considered. Default: ungapped. Default: 0.

       --seed (unsigned 64 bit integer)
              Define seed for the minimisers. Default: 0.

       -o, --out (std::filesystem::path)
              Directory, where output files should be saved. Default: "./".

       -t, --threads (unsigned 8 bit integer)
              Number of threads to use. Default: 1. Default: 1.

       -c, --compressed
              If c is set, the IBFS are compressed. Default: Not compressed.

       -f, --fpr (List of double)
              List  of  bin  false positive rate per expression level. If only one is given, then
              that fpr is used for all expression levels. Default: [].

       -e, --expression_thresholds (List of unsigned 16 bit integer)
              Which expression thresholds should be used for constructing the IBFs. Default: [].

       -l, --number_expression_thresholds (unsigned 8 bit integer)
              Number of expression thresholds. Can be set alternatively to expression_thresholds,
              then the expression thresholds are determined automatically. Default: 0.

       -n, --hash (unsigned 64 bit integer)
              Number of hash functions that should be used when constructing one IBF. Default: 1.

       --include (std::filesystem::path)
              Sequence  file  containing  minimizers,  only  those minimizers will be considered.
              Default: "".

       --exclude (std::filesystem::path)
              Sequence file containing minimizers that should not be stored. Default: "".

       --samples (List of signed 32 bit integer)
              Define which samples belong together, sum has to be equal  to  number  of  sequence
              files. Default: Every sequence file is one sample from one experiment. Default: [].

       -p, --paired
              If set, experiments are paired. Default: Not paired.

       --cutoff (List of unsigned 8 bit integer)
              Define  for  each  sample, what number of found minimisers should be considered the
              result of a sequencing error and therefore be ignored. Default:  Every  sample  has
              anautomatically generated cutoff, which is based on the file size. Default: [].

       --experiment-names (bool)
              If set, names of the experiments are stored in a txt file. Default: 0.

       --levels-by-genome (std::filesystem::path)
              Sequence  file  containing minimizers, only those minimizers will be considered for
              determining the expression thresholds. Default: "".

       --ram  If ram is set and multiple  threads  are  used,  the  multithreading  is  more  RAM
              friendly at the cost of being slower.

VERSION

       Last update:
       needle-ibf version:
       SeqAn version: 3.3.0-rc.1