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Minimap2-2.10 (r761)
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@lh3 lh3 released this 27 Mar 15:47
· 428 commits to master since this release
v2.10
2d7ec75

Changes to minimap2:

  • Optionally output the MD tag for compatibility with existing tools (#63,
    #118 and #137).

  • Use SSE compiler flags more precisely to prevent compiling errors on certain
    machines (#127).

  • Added option --min-occ-floor to set a minimum occurrence threshold. Presets
    intended for assembly-to-reference alignment set this option to 100. This
    option alleviates issues with regions having high copy numbers (#107).

  • Exit with non-zero code on file writing errors (e.g. disk full; #103 and
    #132).

  • Added option -y to copy FASTA/FASTQ comments in query sequences to the
    output (#136).

  • Added the asm20 preset for alignments between genomes at 5-10% sequence
    divergence.

  • Changed the band-width in the ava-ont preset from 500 to 2000. Oxford
    Nanopore reads may contain long deletion sequencing errors that break
    chaining.

Changes to mappy, the Python binding:

  • Fixed a typo in Align.seq() (#126).

Changes to paftools.js, the companion script:

  • Command sam2paf now converts the MD tag to cs.

  • Support VCF output for assembly-to-reference variant calling (#109).

This version should produce identical alignment for read overlapping, RNA-seq
read mapping, and genomic read mapping. We have also added a cook book to show
the variety uses of minimap2 on real datasets. Please see cookbook.md in the
minimap2 source code directory.

(2.10: 27 March 2017, r761)

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