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minimap2(1) Bioinformatics tools minimap2(1) 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 tar- get.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 assem- blies 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%. Min- imap2 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. -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 incor- rect given a multi-part index. See also option --split-pre- fix. --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]. Min- imap2 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 tar- get 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 mini- mizers [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 deprecat- ing --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 oc- currence 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 con- cave 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 re- duces 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 lex- icographically 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 -xs- plice/--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 al- gorithm is better for aligning contigs through long INDELs. --rmq-inner NUM Apply full dynamic programming for anchors within distance NUM [1000]. --hard-mask-level Honor option -M and disable a heurstic to save unmapped sub- sequences 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 qua- dratic in the number of seeds. This option makes minimap2 ex- its 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[=no|dna|rna] Enable short-read alignment heuristics [no]. If this option is used with no argument, `dna' is set. In the DNA 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-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. -j FILE Junctions used to extend alignment towards ends of reads []. FILE can be gene annotations in the BED12 format (aka 12-col- umn BED), or intron positions in 5-column BED with the strand column required. BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'. This option is intended for short RNA-seq reads, while --junc-bed for long noisy RNA- seq reads. -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 re- lated region and align again to test small inversions. Min- imap2 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 posi- tives. 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 Penalty of a mismatch involving ambiguous bases [1]. --pairing=strong|weak|no How to pair paired-end reads [strong]. `no' for aligning the two ends in a pair independently with no `properly paired' set. `weak' for aligning the two ends independently and then pairing the hits. `strong' for jointly aligning and pairing the two ends. --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 ac- ceptor 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 ac- curacy 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. --spsc FILE Splice scores []. Each line consists of five fields: 1) con- tig, 2) offset, 3) `+' or `-', 4) `D' or `A', and 5) score, where offset is the number of bases before a splice junction, `D' indicates the line corresponds to a donor site and `A' for an acceptor site. A positive score suggests the junction is preferred and a negative score suggests the junction is not preferred. --spsc0 INT Penalty for positions not in FILE specified by --spsc [5]. Effective with --spsc but not --junc-bed. --spsc-scale FLOAT Scale splice scores in --spsc by FLOAT rounded to the nearest integer [0.7]. --junc-bed FILE Junctions to prefer during base alignment []. Same format as -j. It is NOT recommended to apply this option to short RNA- seq reads. This would increase run time with little improve- ment to junction accuracy. --junc-bonus INT Score bonus for a splice donor or acceptor found in annota- tion [9]. Effective with --junc-bed but not --spsc. --jump-min-match INT Minimum matching length to create a jump [3]. Equivalent to STAR --alignSJDBoverhangMin. --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 perform- ing 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 align- ment the size of the reservoir above NUM. Set 0 to disable [500m]. Input/output options -a Generate CIGAR and output alignments in the SAM format. Min- imap2 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' cus- tom tag. --cs[=short|long] Output the cs tag. If no argument is given, `short' is set. [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 align- ments. --secondary-seq In SAM output, show query sequences for secondary alignments. --write-junc Output splice junctions in 6-column BED: contig name, start, end, read name, score and strand. Score is the sum of donor and acceptor scores, where GT gets 3, GC gets 2 and AT gets 1 at donor sites, while AG gets 3 and AC gets 1 at acceptor sites. Alignments with mapping quality below 10 are ignored. --pass1 FILE Junctions BED file outputted by --write-junc []. Rows with scores lower than 5 are ignored. When both -j and --pass1 are present, junctions in -j are preferred over in --pass1 when there is ambiguity. --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 fre- quently 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 bot- tleneck. 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 ac- cepted. A large NUM helps load balancing in the multi-thread- ing 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 com- mands 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 op- tions applied later will overwrite the values set by -x. Available STR are: map-ont Align noisy long reads of ~10% error rate to a ref- erence 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 bet- ter for accurate Nanopore reads than map-hifi. map-hifi Align PacBio high-fidelity (HiFi) reads to a refer- ence 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 ref- erence 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 se- quence 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 diver- gence 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 de- mote hits to pseudogenes. splice:hq Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq (-xsplice -C5 -O6,24 -B4). splice:sr Spliced alignment for short RNA-seq reads (-xs- plice:hq --frag=yes -m25 -s40 -2K100m --heap- sort=yes --pairing=weak --sr=rna --min-dp-len=20 --secondary=no). sr Short-read alignment without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -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 consist- ing 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 se- quence 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 (with approximate CIGAR strings) | | 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 | | zd | i | Alignment broken due to Z-drop; bit 1: left broken; bit 2: right broken | +-----+------+-------------------------------------------------------------------------+ 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-complex- ity 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 possi- ble to add non-SSE2/NEON support, but it would make minimap2 slower by several times. SEE ALSO miniasm(1), minimap(1), bwa(1). minimap2-2.30 (r1287) 15 June 2025 minimap2(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | OUTPUT FORMAT | LIMITATIONS | SEE ALSO
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