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: 2024-11-07
       needle-ibf version: 1.0.3
       SeqAn version: 3.3.0

URL

       https://github.com/seqan/needle

LEGAL

       needle-ibf Copyright: BSD 3-Clause License
       Author: Mitra Darvish
       SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
       In your academic works please cite: Needle: a fast  and  space-efficient  prefilter  for  estimating  the
       quantification  of very large collections of expression experiments; Mitra Darvish, Enrico Seiler, Svenja
       Mehringer, René Rahn, and Knut Reinert; Bioinformatics, Volume 38, Issue  17,  1  September  2022,  Pages
       4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492
       For full copyright and/or warranty information see --copyright.

needle-ibf 1.0.3                                   2024-11-07                                      NEEDLE-IBF(1)