Skip to content

Minimap2-2.19 (r1057)

Compare
Choose a tag to compare
@lh3 lh3 released this 27 May 01:25
· 172 commits to master since this release

This release includes a few important improvements backported from unimap:

  • Improvement: more contiguous alignment through long INDELs. This is enabled
    by the minigraph chaining algorithm. All asm* presets now use the new
    algorithm. They can find INDELs up to 100kb and may be faster for
    chromosome-long contigs. The default mode and map* presets use this
    algorithm to replace the long-join heuristic.

  • Improvement: better alignment in highly repetitive regions by rescuing
    high-occurrence seeds. If the distance between two adjacent seeds is too
    large, attempt to choose a fraction of high-occurrence seeds in-between.
    Minimap2 now produces fewer clippings and alignment break points in long
    satellite regions.

  • Improvement: allow to specify an interval of k-mer occurrences with -U.
    For repeat-rich genomes, the automatic k-mer occurrence threshold determined
    by -f may be too large and makes alignment impractically slow. The new
    option protects against such cases. Enabled for asm* and map-hifi.

  • New feature: added the map-hifi preset for mapping PacBio High-Fidelity
    (HiFi) reads.

  • Change to the default: apply --cap-sw-mem=100m for genomic alignment.

  • Bugfix: minimap2 could not generate an index file with -xsr (#734).

This release represents the most significant algorithmic change since v2.1 in
2017. With features backported from unimap, minimap2 now has similar power to
unimap for contig alignment. Unimap will remain an experimental project and is
no longer recommended over minimap2. Sorry for reverting the recommendation in
short time.

(2.20: 26 May 2021, r1055)