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BioForge v6.2.2 — Mapping accuracy validated (99.8% on real E. coli)

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@erlanders177 erlanders177 released this 10 Jul 11:06
· 88 commits to main since this release

Fast is worthless if it's wrong — so here's the proof it isn't. No engine
changes; a new benchmark tool + the result in the README.

── Install ──────────────────────────────────────────────────
pip install bioforge (Python >= 3.10, NumPy only)

Added

  • tools/accuracy_vs_minimap2.py — measures mapping ACCURACY on a real genome:
    simulates reads recording each read's true origin, maps with BioForge and
    minimap2, and counts how many land at the correct position (±tolerance). Real
    genomes have repeats — the hard case.

Result (E. coli K-12, 4.64 Mb, 5000 reads, ±50 bp)

  • 5% error: BioForge 99.8% correct · minimap2 99.8% · 99.8% concordance
  • 10% error: BioForge 99.7% · minimap2 99.9%
  • As accurate as minimap2 — not fast-at-the-cost-of-correctness. Honest note: at
    higher error minimap2 is marginally ahead, and this is E. coli scale.