NAME

       needle-count  -  Get  expression  value  depending  on  minimizers.  This  function  is an alternative to
       pseudoaligners like kallisto. It estimates the expression value for all  sequences  in  the  genome  file
       based  on  the  exact  minimiser occurrences of the given sequence files. Please run genome beforehand to
       create the genome file.

POSITIONAL ARGUMENTS

       ARGUMENT-1 (List of std::filesystem::path)
              Please provide at least one sequence file. 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.

       --include (std::filesystem::path)
              Please provide one sequence file with transcripts.

       --genome (std::filesystem::path)
              Please provide one *.genome file created with the genome command. Default: "".

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

VERSION

       Last update: 2024-11-07
       needle-count version: 1.0.3
       SeqAn version: 3.3.0

URL

       https://github.com/seqan/needle

LEGAL

       needle-count 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-count 1.0.3                                 2024-11-07                                    NEEDLE-COUNT(1)