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Miniprot-0.2 (r116)

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@lh3 lh3 released this 13 Sep 02:05
· 147 commits to master since this release
v0.2
014d429

Notable changes:

  • New feature: output GFF3 with option --gff. PAF alignments are embedded in
    ##PAF lines in the output GFF3.

  • Improvement: give a bonus score -B if extension reaches the end of a protein.
    BWA-MEM and minimap2 both have this heuristic.

  • Improvement: pay more effort to the first and the last exons. This increases
    the sensitivity at the cost of performance.

  • Improvement: increased non-canonical splicing penalty -C from 6 to 11. This
    increases overall specificity.

  • Improvement: rank an alignment with the DP score disregarding introns. This
    is to reduce the effect pseudogenes. Minimap2 uses the same strategy.

  • Bug fixes: fixed incorrect CIGAR in corner cases and patched a minor memory
    leak.

This version works on several real datasets to decent accuracy without crashing
or memory leaks. It is ready for more users.

(0.2: 12 September 2022, r116)

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