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: "".