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.
PacBio subreads (map-db):
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)
minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.samOxford 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.samNanopore 2D cDNA-seq
minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.samNanopore 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.
minimap2 -ax sr ref.fa reads-se.fq > aln.sampaired-end alignment
minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sampaired-end alignment
minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam
Full genome/assembly alignment asm5assembly to assembly
minimap2 -ax asm5 ref.fa asm.fa > aln.sam