.PP

minimap2 - mapping and alignment between collections of DNA sequences

* 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

.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.

.TP 10

Minimizer k-mer length [15]

.TP

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

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

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

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

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

List of ALT contigs [null]

.TP

Drop ALT hits by

.I FLOAT

fraction when ranking and computing mapping quality [0.15]

.TP 10

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

Force minimap2 to always use k-mers occurring

.I INT

times or less [0]. In effect, the max occurrence threshold is set to

the

.RI max{ INT ,

.BR -f }.

.TP

Stop chain enlongation if there are no minimizers within

.IR INT -bp

[10000].

.TP

Bandwidth used in chaining and DP-based alignment [500]. This option

approximately controls the maximum gap size.

.TP

Discard chains consisting of

.RI < INT

number of minimizers [3]

.TP

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

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

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

If

.BR no ,

skip query-target pairs wherein the query name is lexicographically greater

than the target name [yes]

.TP

Equivalent to

.RB ' -DP

.BR --dual = no

.BR --no-long-join '.

Primarily used for all-vs-all read overlapping.

.TP

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

Output at most

.I INT

secondary alignments [5]. This option has no effect when

.B -X

is applied.

.TP

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

Maximum fragment length (aka insert size; effective with

.BR -xsr / --frag = yes )

[800]

.TP

Mark as secondary a chain that overlaps with a better chain by

.I FLOAT

or more of the shorter chain [0.5]

.TP

Honor option

.B -M

and disable a heurstic to save unmapped subsequences and disables

.BR --mask-len .

.TP

Keep an alignment if dropping it leaves an unaligned region on query longer than

.IR INT

[inf]. Effective without

.BR --hard-mask-level .

.TP

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

Check up to

.I INT

partial chains during chaining [5000]. This is a heuristic to avoid quadratic

time complexity in the worst case.

.TP

Scale of gap cost during chaining [1.0]

.TP

Disable the long gap patching heuristic. When this option is applied, the

maximum alignment gap is mostly controlled by

.BR -r .

.TP

Fraction of query sequence length required to bridge a long gap [0.5]. A

smaller value helps to recover longer gaps, at the cost of more false gaps.

.TP

Enable the splice alignment mode.

.TP

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

Prefix to create temporary files. Typically used for a multi-part index.

.TP

Whether to enable the fragment mode [no]

.TP

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

Only map to the reverse complement strand of the reference sequences.

.TP

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

Treat two reads in a pair as independent reads. The mate related fields in SAM

are still properly populated.

.TP 10

Matching score [2]

.TP

Mismatching penalty [4]

.TP

Gap open penalty [4,24]. If

.I INT2

is not specified, it is set to

.IR INT1 .

.TP

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

Cost for a non-canonical GT-AG splicing (effective with

.BR --splice )

[0]

.TP

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

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

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

Score bonus when alignment extends to the end of the query sequence [0].

.TP

Score of a mismatch involving ambiguous bases [1].

.TP

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

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

Score bonus for a splice donor or acceptor found in annotation (effective with

.BR --junc-bed )

[9].

.TP

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

Don't filter seeds towards the ends of chains before performing base-level

alignment.

.TP

Skip alignment if the DP matrix size is above

.IR NUM .

Set 0 to disable [0].

.TP 10

Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF

by default.

.TP

Output alignments to

.I FILE

[stdout].

.TP

Ignore base quality in the input file.

.TP

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

SAM read group line in a format like

.B @RG\\\\tID:foo\\\\tSM:bar

[].

.TP

Copy input FASTA/Q comments to output.

.TP

Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.

.TP

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

Output the MD tag (see the SAM spec).

.TP

Output =/X CIGAR operators for sequence match/mismatch.

.TP

In SAM output, use soft clipping for supplementary alignments.

.TP

Integer seed for randomizing equally best hits. Minimap2 hashes

.I INT

and read name when choosing between equally best hits. [11]

.TP

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

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

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

Whether to output secondary alignments [yes]

.TP

Filter out query sequences longer than

.IR NUM .

.TP

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

In SAM, don't output unmapped reads.

.TP

Print version number to stdout

.TP 10

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 9

PacBio/Oxford Nanopore read to reference mapping

.RB ( -Hk19 )

.TP

Slightly more sensitive for Oxford Nanopore to reference mapping

.RB ( -k15 ).

For PacBio reads, HPC minimizers consistently leads to faster performance and

more sensitive results in comparison to normal minimizers. For Oxford Nanopore

data, normal minimizers are better, though not much. The effectiveness of HPC

is determined by the sequencing error mode.

.TP

PacBio HiFi reads to reference mapping

.RB ( -k19

.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k

.BR -U100,500 ).

.TP

Long assembly to reference mapping

.RB ( -k19

.B -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50

.BR --min-occ-floor=100 ).

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

Long assembly to reference mapping

.RB ( -k19

.B -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50

.BR --min-occ-floor=100 ).

Up to 10% sequence divergence.

.TP

Long assembly to reference mapping

.RB ( -k19

.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50

.BR --min-occ-floor=100 ).

Up to 20% sequence divergence.

.TP

PacBio all-vs-all overlap mapping

.RB ( -Hk19

.B -Xw5 -m100 -g10000 --max-chain-skip

.BR 25 ).

.TP

Oxford Nanopore all-vs-all overlap mapping

.RB ( -k15

.B -Xw5 -m100 -g10000 -r2000 --max-chain-skip

.BR 25 ).

Similarly, the major difference from

.B ava-pb

is that this preset is not using HPC minimizers.

.TP

Long-read spliced alignment

.RB ( -k15

.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9

.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

Long-read splice alignment for PacBio CCS reads

.RB ( -xsplice

.B -C5 -O6,24

.BR -B4 ).

.TP

Short single-end reads without splicing

.RB ( -k21

.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20

.B -s40 -g200 -2K50m --heap-sort=yes

.BR --secondary=no ).

.RE

.TP 10

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

Print query names to stderr, mostly to see which query is crashing minimap2.

.TP

Print seed positions to stderr, for debugging only.

.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

.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.

.PP

miniasm(1), minimap(1), bwa(1).