Minimap2 is a fast general-purpose alignment program to map DNA or long mRNA sequences against a large reference database.  It can be used for:

  • mapping of accurate short reads (preferably longer that 100 bases)
  • mapping 1kb genomic reads at error  rate 15% (e.g. PacBio or Oxford Nanopore genomic reads)
  • mapping full-length noisy Direct RNA or cDNA reads
  • mapping and comparing assembly contigs or closely related full chromosomes of hundreds of megabases in length.



Version on CSC's Servers

Minimap 2.9-r720 is available in Taito


Minimap2 starts in Taito with command:


Without any options, minimap2 takes a reference database and a query sequence file as input and produce approximate mapping, without base-level alignment (i.e. no CIGAR), in the PAF format:

minimap2 ref.fa query.fq > approx-mapping.paf

If you wish to get the output in sam format you can use option -a.

For different data types minimap2 needs to be tuned for optimal performance and accuracy.
With option -x you can take in use case specific parameter sets, pre-defined and recommended by the minimap2 developers.
Map long noisy genomic reads (map-pb and map-ont)

PacBio subreads (map-db):
minimap2 -ax map-pb  ref.fa pacbio-reads.fq > aln.sam
Oxford Nanopore reads (map-ont):
minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam 

Map long mRNA/cDNA reads (splice)

PacBio Iso-seq/traditional cDNA
minimap2 -ax splice -uf ref.fa iso-seq.fq > aln.sam
Nanopore 2D cDNA-seq
minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam
Nanopore Direct RNA-seq
minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam


mapping against SIRV control
minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa

Find overlaps between long reads (ava-pb and aca-ont)

PacBio read overlap
minimap2 -x ava-pb  reads.fq reads.fq > ovlp.paf

Oxford Nanopore read overlap

minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf   

Map short accurate genomic reads (sr)
Note, minimap2 does work well with short spliced reads.

single-end alignment
minimap2 -ax sr ref.fa reads-se.fq > aln.sam
paired-end alignment
minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam    
paired-end alignment
minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam 

Full genome/assembly alignment asm5

assembly to assembly
minimap2 -ax asm5 ref.fa asm.fa > aln.sam  




Minimap21 report



Minimap2 home page