Bin Classification

Bins are classified using a multi-signal approach based on geNomad scores, with a hard completeness filter.

geNomad Classification Accuracy

• Plasmid: Precision 70.8%, Sensitivity 89.8% (Camargo et al. 2024). Nearly one third of contigs called plasmid are potentially false positives.
• Virus: MCC 95.3%, F1 97.3%; strong classification.

geNomad runs in default mode so ALL contigs receive plasmid/virus scores where possible. Filtering presets: default (min-score=0.70), conservative (min-score=0.80), relaxed (min-score=0.00).

Important: geNomad output files contain only positive predictions. Contigs not flagged as viral or plasmid do not appear in virus_summary.tsv or plasmid_summary.tsv.

Hard Completeness Filter (>= 50%)

CheckM2 uses ~20,000 KEGG orthologs for chromosomal housekeeping functions (Chklovski et al. 2023). Plasmids and viruses typically do not carry these markers. Therefore, a bin with completeness >= 50% likely contains chromosomal DNA and MAGGIC does not classify it as a pure Plasmid_MAG or Virus_MAG.

When Completeness >= 50%

MAGGIC Classification	Criteria
Mixed_MAG	geNomad plasmid_summary.tsv has contigs with plasmid_score >= 0.75 AND count / total_contigs >= 0.2 (using Binette contig_count as denominator)
Chromosome_MAG	No contigs with plasmid_score >= 0.75, OR plasmid_fraction < 0.2. Also assigned when virus_summary.tsv exists but only proviruses are present

When Completeness < 50%

MAGGIC Classification	Criteria
Virus_MAG	geNomad virus_summary.tsv has any entries (checked first; virus model is most reliable)
Plasmid_MAG	geNomad plasmid_summary.tsv has entries but virus_summary.tsv has none
Chromosome_MAG	Neither geNomad plasmid nor virus summaries have entries

Bacterial_Confidence Thresholds

Level	Completeness	Contamination	ANI	AF
High	>= 90%	< 5%	>= 95%	>= 0.65
Medium	>= 50%	< 10%	>= 80%	>= 0.50
Low	below Medium thresholds

Thresholds are configurable via CLI options: --high-comp, --high-contam, --high-ani, --high-af, --med-comp, --med-contam, --med-ani, --med-af.