# minimap2 2.23


## Minimap2

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database. Typical use cases include: (1)
mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2)
finding overlaps between long reads with error rate up to ~15%; (3)
splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads
against a reference genome; (4) aligning Illumina single- or paired-end reads;
(5) assembly-to-assembly alignment; (6) full-genome alignment between two
closely related species with divergence below ~15%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than
mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more
accurate on simulated long reads and produces biologically meaningful alignment
ready for downstream analyses. For >100bp Illumina short reads, minimap2 is
three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data.
Detailed evaluations are available from the [minimap2
paper](https://doi.org/10.1093/bioinformatics/bty191) or the
[preprint](https://arxiv.org/abs/1708.01492).

Location and version:

```console
$ which minimap2
/local/cluster/bin/minimap2
$ minimap2 --version
2.23-r1111
```

help message:

```console
$ minimap2
Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]
Options:
  Indexing:
    -H           use homopolymer-compressed k-mer (preferrable for PacBio)
    -k INT       k-mer size (no larger than 28) [15]
    -w INT       minimizer window size [10]
    -I NUM       split index for every ~NUM input bases [4G]
    -d FILE      dump index to FILE []
  Mapping:
    -f FLOAT     filter out top FLOAT fraction of repetitive minimizers [0.0002]
    -g NUM       stop chain enlongation if there are no minimizers in INT-bp [5000]
    -G NUM       max intron length (effective with -xsplice; changing -r) [200k]
    -F NUM       max fragment length (effective with -xsr or in the fragment mode) [800]
    -r NUM[,NUM] chaining/alignment bandwidth and long-join bandwidth [500,20000]
    -n INT       minimal number of minimizers on a chain [3]
    -m INT       minimal chaining score (matching bases minus log gap penalty) [40]
    -X           skip self and dual mappings (for the all-vs-all mode)
    -p FLOAT     min secondary-to-primary score ratio [0.8]
    -N INT       retain at most INT secondary alignments [5]
  Alignment:
    -A INT       matching score [2]
    -B INT       mismatch penalty (larger value for lower divergence) [4]
    -O INT[,INT] gap open penalty [4,24]
    -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1]
    -z INT[,INT] Z-drop score and inversion Z-drop score [400,200]
    -s INT       minimal peak DP alignment score [80]
    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]
  Input/Output:
    -a           output in the SAM format (PAF by default)
    -o FILE      output alignments to FILE [stdout]
    -L           write CIGAR with >65535 ops at the CG tag
    -R STR       SAM read group line in a format like '@RG\tID:foo\tSM:bar' []
    -c           output CIGAR in PAF
    --cs[=STR]   output the cs tag; STR is 'short' (if absent) or 'long' [none]
    --MD         output the MD tag
    --eqx        write =/X CIGAR operators
    -Y           use soft clipping for supplementary alignments
    -t INT       number of threads [3]
    -K NUM       minibatch size for mapping [500M]
    --version    show version number
  Preset:
    -x STR       preset (always applied before other options; see minimap2.1 for details) []
                 - map-pb/map-ont - PacBio CLR/Nanopore vs reference mapping
                 - map-hifi - PacBio HiFi reads vs reference mapping
                 - ava-pb/ava-ont - PacBio/Nanopore read overlap
                 - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5% sequence divergence
                 - splice/splice:hq - long-read/Pacbio-CCS spliced alignment
                 - sr - genomic short-read mapping

See `man ./minimap2.1' for detailed description of these and other advanced command-line options.
```

software ref: <https://github.com/lh3/minimap2>  
research ref: <https://doi.org/10.1093/bioinformatics/bty191>