68 lines
1.1 KiB
Groff
68 lines
1.1 KiB
Groff
.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
|
|
* Indexing the target sequences (optional):
|
|
.RS 4
|
|
minimap2
|
|
.RB [ -H ]
|
|
.RB [ -k
|
|
.IR kmer ]
|
|
.RB [ -w
|
|
.IR miniWinSize ]
|
|
.RB [ -I
|
|
.IR batchSize ]
|
|
.B -d
|
|
.I target.mmi
|
|
.I target.fa
|
|
.RE
|
|
|
|
* Long-read alignment 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
|
|
|
|
* Long read overlap without CIGAR:
|
|
.RS 4
|
|
minimap2
|
|
.B -x
|
|
.R ava10k
|
|
.RB [ -t
|
|
.IR nThreads ]
|
|
.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). It works
|
|
efficiently with query sequences from a few kilobases to ~100 megabases in
|
|
length at a error rate ~15%.
|