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 or the
preprint.
Location and version:
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$ which minimap2
/local/cluster/bin/minimap2
$ minimap2 --version
2.23-r1111
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help message:
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$ 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.
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software ref: https://github.com/lh3/minimap2
research ref: https://doi.org/10.1093/bioinformatics/bty191