.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH LEON "1" "May 2018" "leon 1.4.1" "User Commands"
.SH NAME
leon \- reference free compression for NGS reads
.SH OPTIONS
.SS leon options
.TP
\fB\-file\fR
(1 arg) :    input file (e.g. FASTA/FASTQ for compress or .leon file for decompress)
.TP
\fB\-c\fR
(0 arg) :    compression
.TP
\fB\-d\fR
(0 arg) :    decompression
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores (default is the available number of cores)  [default '0']
.TP
\fB\-lossless\fR
(0 arg) :    switch to lossless compression for qualities (default is lossy. lossy has much higher compression rate, and the loss is in fact a gain. lossy is better!)
.SS compression options
.TP
\fB\-kmer\-size\fR
(1 arg) :    size of a kmer  [default '31']
.TP
\fB\-abundance\fR
(1 arg) :    abundance threshold for solid kmers (default inferred)  [default '']
.TP
\fB\-init\-iterator\fR
(0 arg) :    init iterator for ibank mode
.TP
\fB\-seq\-only\fR
(0 arg) :    store dna seq only, header and quals are discarded, will decompress to fasta (same as \fB\-noheader\fR \fB\-noqual\fR)
.TP
\fB\-noheader\fR
(0 arg) :    discard header
.TP
\fB\-noqual\fR
(0 arg) :    discard quality scores
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.