minimap2 2.18 Pairwise aligner for genomic and spliced nucleotide sequences

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%.