.TH minimap 1 "30 June 2017" "minimap2-2.0-r126-pre" "Bioinformatics tools"

.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences

.SH SYNOPSIS
* Index the target sequences (optional):
.RS 4
minimap2
.RB [ -H ]
.RB [ -k
.IR kmer ]
.RB [ -w
.IR miniWinSize ]
.B -d
.I target.mmi
.I target.fa
.RE

* Align with CIGAR:
.RS 4
minimap2
.B -b
.RB [ -x
.IR preset ]
.I target.mmi
.I query.fa
>
.I output.sam
.br
minimap2
.B -c
.RB [ -H ]
.RB [ -k
.IR kmer ]
.RB [ -w
.IR miniWinSize ]
.RB [ ... ]
.I target.fa
.I query.fa
>
.I output.paf
.RE

.SH DESCRIPTION
.PP
Minimap2 is a fast sequence mapping and alignment program that can find
overlaps between long noisy reads, or map long reads or their assemblies to a
reference genome optionally with detailed alignment (i.e. CIGAR). For
reference-based alignment, it works efficiently with query sequences from a few
kilobases to ~100 megabases in length at a error rate ~15%.