Minimap2-2.28 (r1209)

Notable changes to minimap2:

• Bugfix: --MD was not working properly due to the addition of --ds in the
  last release (#1181 and #1182).

• New feature: added an experimental preset lr:hqae for aligning accurate
  long reads back to their assembly. It has been observed that map-hifi and
  lr:hq may produce many wrong alignments around centromeres when accurate
  long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid
  assembly constructed from them. This new preset produces much more accurate
  alignment. It is still experimental and may be subjective to changes in
  future.

• Change: reduced the default --cap-kalloc to 500m to lower the peak
  memory consumption (#855).

Notable changes to mappy:

• Bugfix: mappy option struct was out of sync with minimap2 (#1177).

Minimap2 should output identical alignments to v2.27.

(2.28: 27 March 2024, r1209)