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Fig. 2 | Genome Biology

Fig. 2

From: GUNC: detection of chimerism and contamination in prokaryotic genomes

Fig. 2

GUNC accurately detects chimerism in incrementally challenging simulation scenarios. a Overview of different types of simulation scenarios. Genomes (filled circles) were simulated as mixtures of lineages (horizontal lines) diverging at various taxonomic levels (columns) from clades (void circles) contained in the GUNC reference (solid lines) or not (dashed). See “Methods” for details. b Median CheckM completeness and contamination estimates (dashed lines) diverged from true values (solid lines) with increasing levels of simulated contamination (type 3a in panel a), whereas GUNC estimates of contamination (green; theoretically expected values as blue solid line) and effective number of surplus lineages (purple) were highly accurate. See Figure S2 for an equivalent plot on type 3b genomes. c–f Detection accuracy across simulation scenarios, quantified using F1-scores (y-axis) across increasing levels of simulated contamination (x-axis). Data shown for scenarios 3a (c, d), 3b (e), 4 (f), and 5a (g); full panels for types 3a and 3b in Figure S3. MIMAG criteria were defined as CheckM contamination < 10%, completeness ≥ 50% (medium) and contamination < 5%, completeness > 90% (high); note that MIMAG criteria on rRNA and tRNA presence were not applied; Cont, CheckM contamination; GUNC, default GUNC CSS cutoff of > 0.45

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