minimap2

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 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%