.TH NEEDLE-MINIMISER 1 "" "needle-minimiser " ""
.SH NAME
needle-minimiser \- Calculates minimiser for given experiments.
.SH POSITIONAL ARGUMENTS
.TP
\fBARGUMENT-1\fP (\fIList\fP of \fIstd::filesystem::path\fP)
Please provide at least one sequence file OR provide one file containing all sequence files with the extension '.lst'. Default: []. 
.SH OPTIONS
.SS Basic options:
.TP
\fB-h\fP, \fB--help\fP
Prints the help page.
.TP
\fB-hh\fP, \fB--advanced-help\fP
Prints the help page including advanced options.
.TP
\fB--version\fP
Prints the version information.
.TP
\fB--copyright\fP
Prints the copyright/license information.
.TP
\fB--export-help\fP (std::string)
Export the help page information. Value must be one of [html, man].
.TP
\fB-k\fP, \fB--kmer\fP (\fIunsigned 8 bit integer\fP)
Define k-mer size for the minimisers. Default: 20. Default: 20. 
.TP
\fB-w\fP, \fB--window\fP (\fIunsigned 32 bit integer\fP)
Define window size for the minimisers. Default: 60. Default: 0. 
.TP
\fB--shape\fP (\fIunsigned 64 bit integer\fP)
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. 
.TP
\fB--seed\fP (\fIunsigned 64 bit integer\fP)
Define seed for the minimisers. Default: 0. 
.TP
\fB-o\fP, \fB--out\fP (\fIstd::filesystem::path\fP)
Directory, where output files should be saved. Default: "./". 
.TP
\fB-t\fP, \fB--threads\fP (\fIunsigned 8 bit integer\fP)
Number of threads to use. Default: 1. Default: 1. 
.TP
\fB--include\fP (\fIstd::filesystem::path\fP)
Sequence file containing minimizers, only those minimizers will be considered. Default: "". 
.TP
\fB--exclude\fP (\fIstd::filesystem::path\fP)
Sequence file containing minimizers that should not be stored. Default: "". 
.TP
\fB--samples\fP (\fIList\fP of \fIsigned 32 bit integer\fP)
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: []. 
.TP
\fB-p\fP, \fB--paired\fP
If set, experiments are paired. Default: Not paired.
.TP
\fB--cutoff\fP (\fIList\fP of \fIunsigned 8 bit integer\fP)
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: []. 
.SH VERSION
\fBLast update: \fR
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\fBneedle-minimiser version: \fR
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\fBSeqAn version: \fR3.2.0