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Minimap2-2.25 (r1173)
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@lh3 lh3 released this 25 Apr 16:46
· 56 commits to master since this release
v2.25
4483f89

Notable changes:

  • Improvement: use the miniprot splice model for RNA-seq alignment by default.
    This model considers non-GT-AG splice sites and has slightly higher
    (<0.1%) accuracy and sensitivity on real human data.

  • Change: increased the default -I to 8G such that minimap2 would create a
    uni-part index for a pair of mammalian genomes. This change may increase the
    memory for all-vs-all read overlap alignment given large datasets.

  • New feature: output the sequences in secondary alignments with option
    --secondary-seq (#687).

  • Bugfix: --rmq was not parsed correctly (#1010)

  • Bugfix: possibly incorrect coordinate when applying end bonus to the target
    sequence (#1025). This is a ksw2 bug. It does not affect minimap2 as
    minimap2 is not using the affected feature.

  • Improvement: incorporated several changes for better compatibility with
    Windows (#1051) and for minimap2 integration at Oxford Nanopore Technologies
    (#1048 and #1033).

  • Improvement: output the HD-line in SAM output (#1019).

  • Improvement: check minimap2 index file in mappy to prevent segmentation
    fault for certain indices (#1008).

For genomic sequences, minimap2 should give identical output to v2.24.
Long-read RNA-seq alignment may occasionally differ from previous versions.

(2.25: 25 April 2023, r1173)

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