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Minimap2-2.4 (r555)
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@lh3 lh3 released this 06 Nov 17:55
· 604 commits to master since this release
v2.4
21a46ba

As is planned, this release focuses on fine tuning the base algorithm. Notable
changes include

  • Changed the mapping quality scale to match the scale of BWA-MEM. This makes
    minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real
    short-read data.

  • Improved the accuracy of splice alignment by modeling one additional base
    close to the GT-AG signal. This model is used by default with -x splice.
    For SIRV control data, however, it is recommended to add --splice-flank=no
    to disable this feature as the SIRV splice signals are slightly different.

  • Tuned the parameters for Nanopore Direct RNA reads. The recommended command
    line is -axsplice -k14 -uf (#46).

  • Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This
    bug is very rare but it affects all versions of minimap2. It is also
    recommended to re-index reference genomes created with map-pb. For human,
    two minimizers in an old index are wrong.

  • Changed option -L in sync with the final decision of hts-specs: a fake
    CIGAR takes the form of <readLen>S<refLen>N. Note that -L only enables
    future tools to recognize long CIGARs. It is not possible for older tools to
    work with such alignments in BAM (#43 and #51).

  • Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate
    alignment.

The minimap2 technical note has also been updated to reflect recent changes.

(2.4: 6 November 2017, r555)

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