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.