Provided by: minimap2_2.27+dfsg-1_amd64 
NAME
minimap2 - mapping and alignment between collections of DNA sequences
SYNOPSIS
* Indexing the target sequences (optional):
minimap2 [-x preset] -d target.mmi target.fa
minimap2 [-H] [-k kmer] [-w miniWinSize] [-I batchSize] -d target.mmi target.fa
* Long-read alignment with CIGAR:
minimap2 -a [-x preset] target.mmi query.fa > output.sam
minimap2 -c [-H] [-k kmer] [-w miniWinSize] [...] target.fa query.fa > output.paf
* Long-read overlap without CIGAR:
minimap2 -x ava-ont [-t nThreads] target.fa query.fa > output.paf
DESCRIPTION
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.
OPTIONS
Indexing options
-k INT Minimizer k-mer length [15]
-w INT Minimizer window size [10]. A minimizer is the smallest k-mer in a window of w consecutive k-
mers.
-j INT Syncmer submer size [10]. Option -j and -w will override each: if -w is applied after -j, -j
will have no effect, and vice versa.
-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.
-I NUM Load at most NUM target bases into RAM for indexing [8G]. If there are more than NUM bases in
target.fa, minimap2 needs to read query.fa multiple times to map it against each batch of
target sequences. This would create a multi-part index. NUM may be ending with k/K/m/M/g/G.
NB: mapping quality is incorrect given a multi-part index. See also option --split-prefix.
--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 -a or -c. When base-level alignment is not
requested, this option is automatically applied.
-d FILE Save the minimizer index of target.fa to 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 -H, -k, -w, -I will be effectively overridden by
the options stored in the index file.
--alt FILE
List of ALT contigs [null]
--alt-drop FLOAT
Drop ALT hits by FLOAT fraction when ranking and computing mapping quality [0.15]
Mapping options
-f FLOAT|INT1[,INT2]
If fraction, ignore top FLOAT fraction of most frequent minimizers [0.0002]. If integer, ignore
minimizers occuring more than INT1 times. INT2 is only effective in the --sr or -xsr mode,
which sets the threshold for a second round of seeding.
-U INT1[,INT2]
Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold
is max{INT1, min{INT2, -f}}. This option prevents excessively small or large -f estimated from
the input reference. Available since r1034 and deprecating --min-occ-floor in earlier versions
of minimap2.
--q-occ-frac FLOAT
Discard a query minimizer if its occurrence is higher than FLOAT fraction of query minimizers
and than the reference occurrence threshold [0.01]. Set 0 to disable. Available since r1105.
-e INT Sample a high-frequency minimizer every INT basepairs [500].
-g NUM Stop chain enlongation if there are no minimizers within NUM-bp [10k].
-r NUM1[,NUM2]
Bandwidth for chaining and base alignment [500,20k]. NUM1 is used for initial chaining and
alignment extension; NUM2 for RMQ-based re-chaining and closing gaps in alignments.
-n INT Discard chains consisting of <INT number of minimizers [3]
-m INT Discard chains with chaining score <INT [40]. Chaining score equals the approximate number of
matching bases minus a concave gap penalty. It is computed with dynamic programming.
-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.
-P Retain all chains and don't attempt to set primary chains. Options -p and -N have no effect
when this option is in use.
--dual=yes|no
If no, skip query-target pairs wherein the query name is lexicographically greater than the
target name [yes]
-X Equivalent to '-DP --dual=no --no-long-join'. Primarily used for all-vs-all read overlapping.
-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 -M), the chain with a lower
score is secondary to the chain with a higher score. If the ratio of the scores is below
FLOAT, the secondary chain will not be outputted or extended with DP alignment later. This
option has no effect when -X is applied.
-N INT Output at most INT secondary alignments [5]. This option has no effect when -X is applied.
-G NUM Maximum gap on the reference (effective with -xsplice/--splice). This option also changes the
chaining and alignment band width to NUM. Increasing this option slows down spliced alignment.
[200k]
-F NUM Maximum fragment length (aka insert size; effective with -xsr/--frag=yes) [800]
-M FLOAT Mark as secondary a chain that overlaps with a better chain by FLOAT or more of the shorter
chain [0.5]
--rmq=no|yes
Use the minigraph chaining algorithm [no]. The minigraph algorithm is better for aligning
contigs through long INDELs.
--hard-mask-level
Honor option -M and disable a heurstic to save unmapped subsequences and disables --mask-len.
--mask-len NUM
Keep an alignment if dropping it leaves an unaligned region on query longer than INT [inf].
Effective without --hard-mask-level.
--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 INT to a large number to switch
off this heurstics.
--max-chain-iter INT
Check up to INT partial chains during chaining [5000]. This is a heuristic to avoid quadratic
time complexity in the worst case.
--chain-gap-scale FLOAT
Scale of gap cost during chaining [1.0]
--no-long-join
Disable the long gap patching heuristic. When this option is applied, the maximum alignment gap
is mostly controlled by -r.
--splice Enable the splice alignment mode.
--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.
--split-prefix STR
Prefix to create temporary files. Typically used for a multi-part index.
--frag=no|yes
Whether to enable the fragment mode [no]
--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.
--rev-only
Only map to the reverse complement strand of the reference sequences.
--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]
--no-pairing
Treat two reads in a pair as independent reads. The mate related fields in SAM are still
properly populated.
--no-hash-name
Produce the same alignment for identical sequences regardless of their sequence names.
Alignment options
-A INT Matching score [2]
-B INT Mismatching penalty [4]
-b INT Mismatching penalty for transitions [same as -B].
-O INT1[,INT2]
Gap open penalty [4,24]. If INT2 is not specified, it is set to INT1.
-E INT1[,INT2]
Gap extension penalty [2,1]. A gap of length k costs min{O1+k*E1,O2+k*E2}. In the splice mode,
the second gap penalties are not used.
-J INT Splice model [1]. 0 for the original minimap2 splice model that always penalizes non-GT-AG
splicing; 1 for the miniprot model that considers non-GT-AG. Option -C has no effect with the
default -J1. -J0.
-C INT Cost for a non-canonical GT-AG splicing (effective with --splice -J0) [0].
-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 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 INT1. Decrease INT2 to find small inversions at the cost of performance and false
positives. Increase INT1 to improves the contiguity of alignment at the cost of poor alignment
in the middle.
-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.
-u CHAR How to find canonical splicing sites GT-AG - f: transcript strand; b: both strands; n: no
attempt to match GT-AG [n]
--end-bonus INT
Score bonus when alignment extends to the end of the query sequence [0].
--score-N INT
Score of a mismatch involving ambiguous bases [1].
--splice-flank=yes|no
Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the
preceding base to a 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
--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 --splice-flank=no to the
command line.
--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' [].
--junc-bonus INT
Score bonus for a splice donor or acceptor found in annotation (effective with --junc-bed) [9].
--end-seed-pen INT
Drop a terminal anchor if s<log(g)+INT, where s is the local alignment score around the anchor
and g the length of the terminal gap in the chain. This option is only effective with --splice.
It helps to avoid tiny terminal exons. [6]
--no-end-flt
Don't filter seeds towards the ends of chains before performing base-level alignment.
--cap-sw-mem NUM
Skip alignment if the DP matrix size is above NUM. Set 0 to disable [100m].
--cap-kalloc NUM
Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir
above NUM. Set 0 to disable [0].
Input/output options
-a Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF by default.
-o FILE Output alignments to FILE [stdout].
-Q Ignore base quality in the input file.
-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.
-R STR SAM read group line in a format like @RG\tID:foo\tSM:bar [].
-y Copy input FASTA/Q comments to output.
-c Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
--cs[=STR]
Output the cs tag. STR can be either short or long. If no STR is given, short is assumed.
[none]
--MD Output the MD tag (see the SAM spec).
--eqx Output =/X CIGAR operators for sequence match/mismatch.
-Y In SAM output, use soft clipping for supplementary alignments.
--secondary-seq
In SAM output, show query sequences for secondary alignments.
--seed INT
Integer seed for randomizing equally best hits. Minimap2 hashes INT and read name when choosing
between equally best hits. [11]
-t INT Number of threads [3]. Minimap2 uses at most three threads when indexing target sequences, and
uses up to INT+1 threads when mapping (the extra thread is for I/O, which is frequently idle
and takes little CPU time).
-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.
-K NUM Number of bases loaded into memory to process in a mini-batch [500M]. Similar to option -I,
K/M/G/k/m/g suffix is accepted. A large NUM helps load balancing in the multi-threading mode,
at the cost of increased memory.
--secondary=yes|no
Whether to output secondary alignments [yes]
--max-qlen NUM
Filter out query sequences longer than NUM.
--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.
--sam-hit-only
In SAM, don't output unmapped reads.
--version Print version number to stdout
Preset options
-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 -x. Available STR
are:
map-ont Align noisy long reads of ~10% error rate to a reference genome. This is the default
mode.
lr:hq Align accurate long reads (error rate <1%) to a reference genome (-k19 -w19 -U50,500
-g10k). This was recommended by ONT developers for recent Nanopore reads produced
with chemistry v14 that can reach ~99% in accuracy. It was shown to work better for
accurate Nanopore reads than map-hifi.
map-hifi Align PacBio high-fidelity (HiFi) reads to a reference genome (-xlr:hq -A1 -B4 -O6,26
-E2,1 -s200). It differs from lr:hq only in scoring. It has not been tested whether
lr:hq would work better for PacBio HiFi reads.
map-pb Align older PacBio continuous long (CLR) reads to a reference genome (-Hk19). Note
that this data type is effectively deprecated by HiFi. Unless you work on very old
data, you probably want to use map-hifi or lr:hq.
map-iclr Align Illumina Complete Long Reads (ICLR) to a reference genome (-k19 -B6 -b4
-O10,50). This was recommended by Illumina developers.
asm5 Long assembly to reference mapping (-k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19
-O39,81 -E3,1 -s200 -z200 -N50). Typically, the alignment will not extend to regions
with 5% or higher sequence divergence. Use this preset if the average divergence is
not much higher than 0.1%.
asm10 Long assembly to reference mapping (-k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9
-O16,41 -E2,1 -s200 -z200 -N50). Use this if the average divergence is around 1%.
asm20 Long assembly to reference mapping (-k19 -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4
-O6,26 -E2,1 -s200 -z200 -N50). Use this if the average divergence is around several
percent.
splice Long-read spliced alignment (-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9
-z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1)
long deletions are taken as introns and represented as the `N' CIGAR operator; 2)
long insertions are disabled; 3) deletion and insertion gap costs are different
during chaining; 4) the computation of the `ms' tag ignores introns to demote hits to
pseudogenes.
splice:hq Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq (-xsplice
-C5 -O6,24 -B4).
sr Short-read alignment without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32
-E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m25 -s40 -g100 -2K50m --heap-sort=yes
--secondary=no).
ava-pb PacBio CLR all-vs-all overlap mapping (-Hk19 -Xw5 -e0 -m100).
ava-ont Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -e0 -m100 -r2k).
Miscellaneous options
--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.
--print-qname
Print query names to stderr, mostly to see which query is crashing minimap2.
--print-seeds
Print seed positions to stderr, for debugging only.
OUTPUT FORMAT
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:
┌────┬────────┬─────────────────────────────────────────────────────────┐
│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) │
└────┴────────┴─────────────────────────────────────────────────────────┘
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:
┌────┬──────┬───────────────────────────────────────────────────────┐
│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 │
└────┴──────┴───────────────────────────────────────────────────────┘
The cs tag encodes difference sequences in the short form or the entire query AND reference sequences in
the long form. It consists of a series of operations:
┌───┬────────────────────────────┬─────────────────────────────────┐
│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 │
└───┴────────────────────────────┴─────────────────────────────────┘
LIMITATIONS
* 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.
* 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.
SEE ALSO
miniasm(1), minimap(1), bwa(1).