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
    readsagainst 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%

WWW: https://github.com/lh3/minimap2