Additional file 1 of BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
Creators: name: Pavia, Michael J.
name: Chede, Abhinav
name: Wu, Zijun
name: Cadillo-Quiroz, Hinsby
name: Zhu, Qiyun
Publisher: name: figshare
Year: 2023
Subjects: subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences
subject: Information Systems

description: Additional file 1: Fig. S1. Correlation between completeness (A) and redundancy (contamination) (B) values calculated by BinaRena and CheckM. A total of 596 bins recovered by MaxBin and MetaBAT from the MAQ dataset were evaluated. The CheckM marker gene set for domain Bacteria was used, which contains 104 genes arranged in 58 sets. The regression line (black) is plotted in each panel. The Pearson’s correlation coefficient (r) and its p-value are marked under the plot. Fig. S2. Sulfotelmatobacter MAGs identified by three automatic binners. Scatter plots were defined by t-SNE on k-mer (k = 6) frequencies. Marker size (radius) is proportional to contig length. Marker opacity is proportional to the cube root of contig coverage in location 3 at depth of 20cm. A. MaxBin’s result. B, C. MetaBAT’s results. D, E. DASTool’s results which are both subsets of MaxBin results. D came from a bin with high redundancy (contamination) (40.89%) and only classified to the family level (Koribacteraceae) and E is a subset of panel A. F. Multi-panel scatter plot representing contig coverage across metagenomes for curated Sulfotelmatobacter MAG. Gray circles represent contigs without dsrAB, while the red circle represents the potentially misplaced contigs with dsrAB. Fig. S3. Various views of the TD metagenome #76. Three dimensionality reduction methods, PCA, t-SNE, and UMAP, were applied to k-mer frequency profiles with k = 4, 5, and 6. In addition, the coverage (log) was plotted against GC content and contig length (log). Marker size (radius) is proportional to the cube root of contig length. Except for the last two plots (in which contig coverage is the y-axis), marker opacity is proportional to the square root of contig coverage. Colors are assigned to the top nine most abundant families. The color codes are identical to that of Fig. 3A, B. Fig. S4. Comparison of an Escherichia MAG identified by three automatic binners. Scatter plots were defined by t-SNE on k-mer (k = 6) frequencies. Marker size (radius) is proportional to the cube root of contig length. Marker opacity is proportional to the square root of contig coverage. A. MaxBin’s result (see also Fig. 3G), which has the highest consistency with the manually identified MAG (Fig. 3F). B. MetaBAT’s result (also DASTool’s primary result), which contains a proportion of the Escherichia contigs plus a separate contig cluster assigned to genus Faecalibacterium (dashed circle). C. DASTool’s secondary result (equivalent to the MaxBin bin excluding the MetaBAT bin). Fig. S5. Recovery of a pathogenic Escherichia coli MAG from TD sample #50076 (19.82 Gbp raw reads, 9,816 contigs totaling 62.2 Mbp), which contains multiple E. coli strains. Scatter plot was defined by t-SNE on k-mer (k = 6) frequencies. Marker size (radius) is proportional to the cube root of contig length. Marker opacity is proportional to the cube root of contig coverage. Colors were assigned to the top 14 most abundant genera in the sample. A. View of the entire assembly. A cluster of contigs mainly assigned to Escherichia was selected (dashed polygon). B. The selected cluster of contigs. Its coverage profile exhibits a multi-modal pattern (inset of A). Therefore, the top five out of 20 bins of the histogram were retained. C. The retained contigs, which represent a putative E. coli MAG. Table S1. Comparison of functionality of BinaRena and Elviz. Table S2. Metrics of contig clusters / bins in TD sample #76 calculated by BinaRena. Table S3. Metrics of contig clusters / bins in TD sample #50076 calculated by BinaRena.