Fig. 2

Identification of high-quality bins in comparative assemblies highlights the need for dereplication of different binning methods. a Binning performed by Metabat (light blue) and Proximeta Hi-C binning (Hi-C; blue) revealed that the long-read assembly consistently had fewer, longer contigs per bin than a short-read assembly. b Bin set division into medium-quality draft (MQ) and high-quality draft (HQ) bins was based on DAS_Tool single-copy gene (SCG) redundancy and completeness. Assessment of SCG completeness and redundancy revealed 10 and 42 high-quality bins in the long-read (c) and short-read (d) assemblies, respectively. The Proximeta Hi-C binning method performed better in terms of SCG metrics in the long-read assembly. e Plots of all of identified bins in the long-read (triangle) and short-read (circle) assemblies revealed a wide range of chimeric bins containing high SCG redundancy. Bins highlighted in the blue rectangle correspond to the MQ bins identified by the DAS_tool algorithm while the red rectangle corresponds to the HQ bin set