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