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%.