Issues

• ONT R10 amplicon span-length shape and strand-specific error rates miss the PRJEB92208 targets

  berntpopp/MucOneUp#131 · Filter by author berntpopp opened on Sep 24, 2026

• enhancement(profiles): resolve the read profile once and verify its sha256

  enhancement
  berntpopp/MucOneUp#128 · Filter by author berntpopp opened on Sep 23, 2026

• bug(amplicon): inserted coverage default shadows pacbio_params.coverage

  bug
  berntpopp/MucOneUp#125 · Filter by author berntpopp opened on Sep 23, 2026

• chore(amplicon): metadata, intermediate-file, model-doc and version-probe housekeeping

  bugdocumentation
  berntpopp/MucOneUp#110 · Filter by author berntpopp opened on Sep 23, 2026

• feat(reads): calibrated molecule model (homopolymer stutter, PCR smear, chimeras, concatemers, off-target) via read profiles

  enhancement
  berntpopp/MucOneUp#103 · Filter by author berntpopp opened on Sep 23, 2026

• bug(reads): amplicon reads are simulated from one strand only

  bug
  berntpopp/MucOneUp#101 · Filter by author berntpopp opened on Sep 23, 2026

• feat(reads): per-read truth manifest and unique read names for amplicon simulation

  bugenhancement
  berntpopp/MucOneUp#100 · Filter by author berntpopp opened on Sep 23, 2026

• VNTR downsample mode produces unrealistic coverage: simulation architecture doesn't generate flanking reads

  berntpopp/MucOneUp#88 · Filter by author berntpopp opened on Apr 6, 2026

• Feature: Evaluate GENOMICON-Seq for realistic PCR duplicate simulation

  enhancement
  berntpopp/MucOneUp#52 · Filter by author berntpopp opened on Nov 23, 2025
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