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Minimap2-2.3 (r531)
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@lh3 lh3 released this 23 Oct 03:17
· 628 commits to master since this release
v2.3
306e454

This release comes with many improvements and bug fixes:

  • The sr preset now supports paired-end short-read alignment. Minimap2 is
    3-4 times as fast as BWA-MEM, but is slightly less accurate on simulated
    reads.

  • Meticulous improvements to assembly-to-assembly alignment (special thanks to
    Alexey Gurevich from the QUAST team): a) apply a small penalty to matches
    between ambiguous bases; b) reduce missing alignments due to spurious
    overlaps; c) introduce the short form of the cs tag, an improvement to the
    SAM MD tag.

  • Make sure gaps are always left-aligned.

  • Recognize U bases from Oxford Nanopore Direct RNA-seq (#33).

  • Fixed slightly wrong chaining score. Fixed slightly inaccurate coordinates
    for split alignment.

  • Fixed multiple reported bugs: 1) wrong reference name for inversion
    alignment (#30); 2) redundant SQ lines when multiple query files are
    specified (#39); 3) non-functioning option -K (#36).

This release has implemented all the major features I planned five months ago,
plus the addition of spliced long-read alignment. The next couple of releases
will focus on fine tuning the base algorithm.

(2.3: 22 October 2017, r531)

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