.TH minimap2 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
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). At present,
it works efficiently with query sequences from a few kilobases to ~100
megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
SAM format.

.SH OPTIONS

.SS Indexing options

.TP 10
.BI -k \ INT
Minimizer k-mer length [17]

.TP
.BI -w \ INT
Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
in a window of w consecutive k-mers.

.TP
.B -H
Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
contracting homopolymer runs to a single base. An HPC minimizer is a minimizer
on the HPC sequence.

.TP
.BI -I \ NUM
Load at most
.I NUM
target bases into RAM for indexing [4G]. If there are more than
.I NUM
bases in
.IR target.fa ,
minimap2 needs to read
.I query.fa
multiple times to map it against each batch of target sequences.
.I NUM
may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
multi-part index.

.TP
.BI -d \ FILE
Save the minimizer index of
.I target.fa
to
.I FILE
[no dump]

.SS Mapping options

.TP 10
.BI -f \ FLOAT
Ignore top
.I FLOAT
fraction of most frequent minimizers [0.0002]

.SH OUTPUT FORMAT

.TS
center box;
cb | cb | cb
r | c | l .
Col	Type	Description
_
1	string	Query sequence name
2	int	Query sequence length
3	int	Query start coordinate (0-based)
4	int	Query end coordinate (0-based)
5	char	`+' if query and target on the same strand; `-' if opposite
6	string	Target sequence name
7	int	Target sequence length
8	int	Target start coordinate on the original strand
9	int	Target end coordinate on the original strand
10	int	Number of matching bases in the mapping
11	int	Number bases, including gaps, in the mapping
12	int	Mapping quality (0-255 with 255 for missing)
.TE

.SH SEE ALSO
.PP
miniasm(1), minimap(1), bwa(1).