v0.3.0

Multi-lineage mixture support for wastewater samples

Real wastewater samples contain multiple co-circulating norovirus genotypes. This release adds the ability to simulate these mixtures directly.

New features

• --preset flag with 4 built-in mixture profiles: us-2024 (CaliciNet 2024-25, PMC12205451), diverse, gi-dominant, outbreak
• --mixture flag for custom genotype proportions, e.g. "GII.17:0.75,GII.4:0.25"
• Per-sample mixture syntax in the TSV genotype column (e.g. GII.17:0.75,GII.4:0.15,GI.1:0.10)
• Per-lineage ground truth in summary TSV (lineage_detail column) and manifest JSON (per_lineage section)
• Weighted aggregate coverage stats across lineages
• Example wastewater sample sheet at data/samples_mixture.tsv

Quickstart

nocasim simulate \
  --sample-sheet samples.tsv \
  --references data/references/ \
  --preset us-2024 \
  --art-modern art_modern \
  --outdir results/

Full backward compatibility — existing single-genotype sample sheets work without changes.