minimap2.1

.TH minimap2 1 "29 April 2023" "minimap2-2.26 (r1175)" "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 [ -x
.IR preset ]
.B -d
.I target.mmi
.I target.fa
.br
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 -a
.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
ava-ont
.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 [15]
.TP
.BI -w \ INT
Minimizer window size [10]. A minimizer is the smallest k-mer
in a window of w consecutive k-mers.
.TP
.BI -j \ INT
Syncmer submer size [10]. Option
.B -j
and
.B -w
will override each: if
.B -w
is applied after
.BR -j ,
.B -j
will have no effect, and vice versa.

.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 [8G]. 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. This would create a multi-part index.
.I NUM
may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
multi-part index. See also option
.BR --split-prefix .
.TP
.B --idx-no-seq
Don't store target sequences in the index. It saves disk space and memory but
the index generated with this option will not work with
.B -a
or
.BR -c .
When base-level alignment is not requested, this option is automatically applied.
.TP
.BI -d \ FILE
Save the minimizer index of
.I target.fa
to
.I FILE
[no dump]. Minimap2 indexing is fast. It can index the human genome in a couple
of minutes. If even shorter startup time is desired, use this option to save
the index. Indexing options are fixed in the index file. When an index file is
provided as the target sequences, options
.BR -H ,
.BR -k ,
.BR -w ,
.B -I
will be effectively overridden by the options stored in the index file.
.TP
.BI --alt \ FILE
List of ALT contigs [null]
.TP
.BI --alt-drop \ FLOAT
Drop ALT hits by
.I FLOAT
fraction when ranking and computing mapping quality [0.15]
.SS Mapping options
.TP 10
.BI -f \ FLOAT | INT1 [, INT2 ]
If fraction, ignore top
.I FLOAT
fraction of most frequent minimizers [0.0002]. If integer,
ignore minimizers occuring more than
.I INT1
times.
.I INT2
is only effective in the
.B --sr
or
.B -xsr
mode, which sets the threshold for a second round of seeding.
.TP
.BI -U \ INT1 [, INT2 ]
Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
.RI max{ INT1 ,\ min{ INT2 ,
.BR -f }}.
This option prevents excessively small or large
.B -f
estimated from the input reference. Available since r1034 and deprecating
.B --min-occ-floor
in earlier versions of minimap2.
.TP
.BI --q-occ-frac \ FLOAT
Discard a query minimizer if its occurrence is higher than
.I FLOAT
fraction of query minimizers and than the reference occurrence threshold
[0.01]. Set 0 to disable. Available since r1105.
.TP
.BI -e \ INT
Sample a high-frequency minimizer every
.I INT
basepairs [500].
.TP
.BI -g \ NUM
Stop chain enlongation if there are no minimizers within
.IR NUM -bp
[10k].
.TP
.BI -r \ NUM1 [, NUM2 ]
Bandwidth for chaining and base alignment [500,20k].
.I NUM1
is used for initial chaining and alignment extension;
.I NUM2
for RMQ-based re-chaining and closing gaps in alignments.
.TP
.BI -n \ INT
Discard chains consisting of
.RI < INT
number of minimizers [3]
.TP
.BI -m \ INT
Discard chains with chaining score
.RI < INT
[40]. Chaining score equals the approximate number of matching bases minus a
concave gap penalty. It is computed with dynamic programming.
.TP
.B -D
If query sequence name/length are identical to the target name/length, ignore
diagonal anchors. This option also reduces DP-based extension along the
diagonal.
.TP
.B -P
Retain all chains and don't attempt to set primary chains. Options
.B -p
and
.B -N
have no effect when this option is in use.
.TP
.BR --dual = yes | no
If
.BR no ,
skip query-target pairs wherein the query name is lexicographically greater
than the target name [yes]
.TP
.B -X
Equivalent to
.RB ' -DP
.BR --dual = no
.BR --no-long-join '.
Primarily used for all-vs-all read overlapping.
.TP
.BI -p \ FLOAT
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
Between two chains overlaping over half of the shorter chain (controlled by
.BR -M ),
the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
.IR FLOAT ,
the secondary chain will not be outputted or extended with DP alignment later.
This option has no effect when
.B -X
is applied.
.TP
.BI -N \ INT
Output at most
.I INT
secondary alignments [5]. This option has no effect when
.B -X
is applied.
.TP
.BI -G \ NUM
Maximum gap on the reference (effective with
.BR -xsplice / --splice ).
This option also changes the chaining and alignment band width to
.IR NUM .
Increasing this option slows down spliced alignment. [200k]
.TP
.BI -F \ NUM
Maximum fragment length (aka insert size; effective with
.BR -xsr / --frag = yes )
[800]
.TP
.BI -M \ FLOAT
Mark as secondary a chain that overlaps with a better chain by
.I FLOAT
or more of the shorter chain [0.5]
.TP
.BR --rmq = no | yes
Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
for aligning contigs through long INDELs.
.TP
.B --hard-mask-level
Honor option
.B -M
and disable a heurstic to save unmapped subsequences and disables
.BR --mask-len .
.TP
.BI --mask-len \ NUM
Keep an alignment if dropping it leaves an unaligned region on query longer than
.IR INT
[inf]. Effective without
.BR --hard-mask-level .
.TP
.BI --max-chain-skip \ INT
A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming
for chaining. The time complexity is quadratic in the number of seeds. This
option makes minimap2 exits the inner loop if it repeatedly sees seeds already
on chains. Set
.I INT
to a large number to switch off this heurstics.
.TP
.BI --max-chain-iter \ INT
Check up to
.I INT
partial chains during chaining [5000]. This is a heuristic to avoid quadratic
time complexity in the worst case.
.TP
.BI --chain-gap-scale \ FLOAT
Scale of gap cost during chaining [1.0]
.TP
.B --no-long-join
Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by
.BR -r .
.TP
.B --splice
Enable the splice alignment mode.
.TP
.B --sr
Enable short-read alignment heuristics. In the short-read mode, minimap2
applies a second round of chaining with a higher minimizer occurrence threshold
if no good chain is found. In addition, minimap2 attempts to patch gaps between
seeds with ungapped alignment.
.TP
.BI --split-prefix \ STR
Prefix to create temporary files. Typically used for a multi-part index.
.TP
.BR --frag = no | yes
Whether to enable the fragment mode [no]
.TP
.B --for-only
Only map to the forward strand of the reference sequences. For paired-end
reads in the forward-reverse orientation, the first read is mapped to forward
strand of the reference and the second read to the reverse stand.
.TP
.B --rev-only
Only map to the reverse complement strand of the reference sequences.
.TP
.BR --heap-sort = no | yes
If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
faster for short reads, but slower for long reads. [no]
.TP
.B --no-pairing
Treat two reads in a pair as independent reads. The mate related fields in SAM
are still properly populated.
.TP
.B --no-hash-name
Produce the same alignment for identical sequences regardless of their sequence names.
.SS Alignment options
.TP 10
.BI -A \ INT
Matching score [2]
.TP
.BI -B \ INT
Mismatching penalty [4]
.TP
.BI -O \ INT1[,INT2]
Gap open penalty [4,24]. If
.I INT2
is not specified, it is set to
.IR INT1 .
.TP
.BI -E \ INT1[,INT2]
Gap extension penalty [2,1]. A gap of length
.I k
costs
.RI min{ O1 + k * E1 , O2 + k * E2 }.
In the splice mode, the second gap penalties are not used.
.TP
.BI -C \ INT
Cost for a non-canonical GT-AG splicing (effective with
.BR --splice )
[0]
.TP
.BI -z \ INT1[,INT2]
Truncate an alignment if the running alignment score drops too quickly along
the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the
drop of score is above
.IR INT2 ,
minimap2 will reverse complement the query in the related region and align
again to test small inversions. Minimap2 truncates alignment if there is an
inversion or the drop of score is greater than
.IR INT1 .
Decrease
.I INT2
to find small inversions at the cost of performance and false positives.
Increase
.I INT1
to improves the contiguity of alignment at the cost of poor alignment in the
middle.
.TP
.BI -s \ INT
Minimal peak DP alignment score to output [40]. The peak score is computed from
the final CIGAR. It is the score of the max scoring segment in the alignment
and may be different from the total alignment score.
.TP
.BI -u \ CHAR
How to find canonical splicing sites GT-AG -
.BR f :
transcript strand;
.BR b :
both strands;
.BR n :
no attempt to match GT-AG [n]
.TP
.BI --end-bonus \ INT
Score bonus when alignment extends to the end of the query sequence [0].
.TP
.BI --score-N \ INT
Score of a mismatch involving ambiguous bases [1].
.TP
.BR --splice-flank = yes | no
Assume the next base to a
.B GT
donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
base to a
.B AG
acceptor tends to be C/T [no].
This trend is evolutionarily conservative, all the way to S. cerevisiae
(PMID:18688272). Specifying this option generally leads to higher junction
accuracy by several percents, so it is applied by default with
.BR --splice .
However, the SIRV control does not honor this trend
(only ~60%). This option reduces accuracy. If you are benchmarking minimap2
on SIRV data, please add
.B --splice-flank=no
to the command line.
.TP
.BR --junc-bed \ FILE
Gene annotations in the BED12 format (aka 12-column BED), or intron positions
in 5-column BED. With this option, minimap2 prefers splicing in annotations.
BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'
[].
.TP
.BR --junc-bonus \ INT
Score bonus for a splice donor or acceptor found in annotation (effective with
.BR --junc-bed )
[9].
.TP
.BI --end-seed-pen \ INT
Drop a terminal anchor if
.IR s <log( g )+ INT ,
where
.I s
is the local alignment score around the anchor and
.I g
the length of the terminal gap in the chain. This option is only effective
with
.BR --splice .
It helps to avoid tiny terminal exons. [6]
.TP
.B --no-end-flt
Don't filter seeds towards the ends of chains before performing base-level
alignment.
.TP
.BI --cap-sw-mem \ NUM
Skip alignment if the DP matrix size is above
.IR NUM .
Set 0 to disable [100m].
.TP
.BI --cap-kalloc \ NUM
Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
.IR NUM .
Set 0 to disable [0].
.SS Input/output options
.TP 10
.B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.
.TP
.BI -o \ FILE
Output alignments to
.I FILE
[stdout].
.TP
.B -Q
Ignore base quality in the input file.
.TP
.B -L
Write CIGAR with >65535 operators at the CG tag. Older tools are unable to
convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM
compatible with older tools. Newer tools recognizes this tag and reconstruct
the real CIGAR in memory.
.TP
.BI -R \ STR
SAM read group line in a format like
.B @RG\\\\tID:foo\\\\tSM:bar
[].
.TP
.B -y
Copy input FASTA/Q comments to output.
.TP
.B -c
Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
.TP
.BI --cs[= STR ]
Output the
.B cs
tag.
.I STR
can be either
.I short
or
.IR long .
If no
.I STR
is given,
.I short
is assumed. [none]
.TP
.B --MD
Output the MD tag (see the SAM spec).
.TP
.B --eqx
Output =/X CIGAR operators for sequence match/mismatch.
.TP
.B -Y
In SAM output, use soft clipping for supplementary alignments.
.TP
.B --secondary-seq
In SAM output, show query sequences for secondary alignments.
.TP
.BI --seed \ INT
Integer seed for randomizing equally best hits. Minimap2 hashes
.I INT
and read name when choosing between equally best hits. [11]
.TP
.BI -t \ INT
Number of threads [3]. Minimap2 uses at most three threads when indexing target
sequences, and uses up to
.IR INT +1
threads when mapping (the extra thread is for I/O, which is frequently idle and
takes little CPU time).
.TP
.B -2
Use two I/O threads during mapping. By default, minimap2 uses one I/O thread.
When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O
thread may become the bottleneck. Apply this option to use one thread for input
and another thread for output, at the cost of increased peak RAM.
.TP
.BI -K \ NUM
Number of bases loaded into memory to process in a mini-batch [500M].
Similar to option
.BR -I ,
K/M/G/k/m/g suffix is accepted. A large
.I NUM
helps load balancing in the multi-threading mode, at the cost of increased
memory.
.TP
.BR --secondary = yes | no
Whether to output secondary alignments [yes]
.TP
.BI --max-qlen \ NUM
Filter out query sequences longer than
.IR NUM .
.TP
.B --paf-no-hit
In PAF, output unmapped queries; the strand and the reference name fields are
set to `*'. Warning: some paftools.js commands may not work with such output
for the moment.
.TP
.B --sam-hit-only
In SAM, don't output unmapped reads.
.TP
.B --version
Print version number to stdout
.SS Preset options
.TP 10
.BI -x \ STR
Preset []. This option applies multiple options at the same time. It should be
applied before other options because options applied later will overwrite the
values set by
.BR -x .
Available
.I STR
are:
.RS
.TP 10
.B map-ont
Align noisy long reads of ~10% error rate to a reference genome. This is the
default mode.
.TP
.B map-hifi
Align PacBio high-fidelity (HiFi) reads to a reference genome
.RB ( -k19
.B -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1
.BR -s200 ).
.TP
.B map-pb
Align older PacBio continuous long (CLR) reads to a reference genome
.RB ( -Hk19 ).
.TP
.B asm5
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
.BR -N50 ).
Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%.
.TP
.B asm10
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
.BR -N50 ).
Up to 10% sequence divergence.
.TP
.B asm20
Long assembly to reference mapping
.RB ( -k19
.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.BR -N50 ).
Up to 20% sequence divergence.
.TP
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
.BR --splice-flank=yes ).
In the splice mode, 1) long deletions are taken as introns and represented as
the
.RB ` N '
CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the
.RB ` ms '
tag ignores introns to demote hits to pseudogenes.
.TP
.B splice:hq
Long-read splice alignment for PacBio CCS reads
.RB ( -xsplice
.B -C5 -O6,24
.BR -B4 ).
.TP
.B sr
Short single-end reads without splicing
.RB ( -k21
.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m25
.B -s40 -g100 -2K50m --heap-sort=yes
.BR --secondary=no ).
.TP
.B ava-pb
PacBio CLR all-vs-all overlap mapping
.RB ( -Hk19
.B -Xw5 -e0
.BR -m100 ).
.TP
.B ava-ont
Oxford Nanopore all-vs-all overlap mapping
.RB ( -k15
.B -Xw5 -e0 -m100
.BR -r2k ).
.RE
.SS Miscellaneous options
.TP 10
.B --no-kalloc
Use the libc default allocator instead of the kalloc thread-local allocator.
This debugging option is mostly used with Valgrind to detect invalid memory
accesses. Minimap2 runs slower with this option, especially in the
multi-threading mode.
.TP
.B --print-qname
Print query names to stderr, mostly to see which query is crashing minimap2.
.TP
.B --print-seeds
Print seed positions to stderr, for debugging only.
.SH OUTPUT FORMAT
.PP
Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
default. PAF is a TAB-delimited text format with each line consisting of at
least 12 fields as are described in the following table:
.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/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

.PP
When alignment is available, column 11 gives the total number of sequence
matches, mismatches and gaps in the alignment; column 10 divided by column 11
gives the BLAST-like alignment identity. When alignment is unavailable,
these two columns are approximate. PAF may optionally have additional fields in
the SAM-like typed key-value format. Minimap2 may output the following tags:
.TS
center box;
cb | cb | cb
r | c | l .
Tag	Type	Description
_
tp	A	Type of aln: P/primary, S/secondary and I,i/inversion
cm	i	Number of minimizers on the chain
s1	i	Chaining score
s2	i	Chaining score of the best secondary chain
NM	i	Total number of mismatches and gaps in the alignment
MD	Z	To generate the ref sequence in the alignment
AS	i	DP alignment score
SA	Z	List of other supplementary alignments
ms	i	DP score of the max scoring segment in the alignment
nn	i	Number of ambiguous bases in the alignment
ts	A	Transcript strand (splice mode only)
cg	Z	CIGAR string (only in PAF)
cs	Z	Difference string
dv	f	Approximate per-base sequence divergence
de	f	Gap-compressed per-base sequence divergence
rl	i	Length of query regions harboring repetitive seeds
.TE

.PP
The
.B cs
tag encodes difference sequences in the short form or the entire query
.I AND
reference sequences in the long form. It consists of a series of operations:
.TS
center box;
cb | cb |cb
r | l | l .
Op	Regex	Description
_
 =	[ACGTN]+	Identical sequence (long form)
 :	[0-9]+	Identical sequence length
 *	[acgtn][acgtn]	Substitution: ref to query
 +	[acgtn]+	Insertion to the reference
 -	[acgtn]+	Deletion from the reference
 ~	[acgtn]{2}[0-9]+[acgtn]{2}	Intron length and splice signal
.TE

.SH LIMITATIONS
.TP 2
*
Minimap2 may produce suboptimal alignments through long low-complexity regions
where seed positions may be suboptimal. This should not be a big concern
because even the optimal alignment may be wrong in such regions.
.TP
*
Minimap2 requires SSE2 or NEON instructions to compile. It is possible to add
non-SSE2/NEON support, but it would make minimap2 slower by several times.
.SH SEE ALSO
.PP
miniasm(1), minimap(1), bwa(1).