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PanBreak 0.2.0

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@yykaya yykaya released this 03 Nov 12:15
v0.2.0
9987f5e

Added

  • panbreak graph --builder minigraph: locus graphs built natively with minigraph (-cxggs), with
    assembly paths from minigraph -cxasm --vc; runs on macOS without containers.
  • panbreak graph --builder cactus: locus graphs built with Minigraph-Cactus (cactus-pangenome) in a
    digest-pinned container or a native install.
  • panbreak convert: imports GFA with P lines, W lines (Minigraph-Cactus, vg) or minigraph rGFA
    with GAF alignments, and extracts a locus from a large graph with odgi (--region).
  • --skip-build (alias of --skip-pggb) reuses the output of any builder.
  • panbreak check lists minigraph and cactus-pangenome and the available graph builders.

Changed

  • bubbles reverses paths that run against the reference orientation.
  • bubbles ignores path events within --cover-pad bp of a path end (unanchored sequence ends);
    results on pggb graphs of the example are unchanged.
  • --trim-up/--trim-down match paths by sample name, so they work with any builder.
  • minigraph is part of the conda environment.

On the synthetic example the three builders give highly consistent results: genotype concordance 99.89 % (pggb), 99.87 % (minigraph) and 99.88 % (Minigraph-Cactus), with 100 % carrier sensitivity and no false carriers. These are preliminary results on toy data; reports from real loci are very welcome as GitHub issues.

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PanBreak 0.1.1

PanBreak 0.1.1

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@yykaya yykaya released this 31 Oct 11:50
v0.1.1
6a9e668

Added

  • panbreak check: reports the Python dependencies and external tools that PanBreak can find, with
    versions and the subcommands that need them.
  • End-to-end test on a toy graph and an unaligned BAM (bubbles → kmers → genotype), run in CI
    and in the conda package test.
  • CI job that installs the conda environment on Linux and macOS (arm64) and builds the conda package
    from the repository.

Changed

  • GFF files with GTF-style attributes (key "value", e.g. liftoff output) are accepted by
    regions and annotate.
  • Insertion clustering across genomes; bubble labels prefer protein-coding genes.
  • Graph layout and haplotype flow plots scale to large panels.
  • Python 3.10 or newer is required; tested with 3.10, 3.12 and 3.13.
  • Package metadata uses an SPDX license expression.

Install from source with conda env create -f environment.yml (see the README). panbreak check lists the tools PanBreak finds.

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