.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH MINIMAP2.PY "1" "June 2020" "minimap2.py 2.17" "User Commands"
.SH NAME
minimap2.py \- minimap2 Python3 interface
.SH SYNOPSIS
.B minimap2.py
[\fI\,options\/\fR] \fI\,<ref.fa>|<ref.mmi> <query.fq>\/\fR
.SH OPTIONS
.TP
\fB\-x\fR STR
preset: sr, map\-pb, map\-ont, asm5, asm10 or splice
.TP
\fB\-n\fR INT
mininum number of minimizers
.TP
\fB\-m\fR INT
mininum chaining score
.TP
\fB\-k\fR INT
k\-mer length
.TP
\fB\-w\fR INT
minimizer window length
.TP
\fB\-r\fR INT
band width
.TP
\fB\-c\fR
output the cs tag
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.