Acknowledgements
This work was supported by the National Natural Science Foundation of China (Grant No. 32071666, 32271552) and the Science & Technology Fundamental Resources Investigation Program (Grant No. 2022FY101000).
Figure 1. A. The interface of GeneMiner-GUI. B. Performance comparison between GeneMiner and aTRAM, Easy353, and HybPiper. The bar graph represents the average values for the speed, memory usage, and disk space usage used by these four tools when analyzing two species,A. thaliana and O. sativa .
Figure 2. The workflow of GeneMiner. A. Filtering reads. B. Assembly. C. Verification.
Figure 3. A. A comparison of the results obtained by aTRAM, Easy353, GeneMiner, and HybPiper for Angiosperms353 genes in A. thaliana (left, light-colored bars) and O. sativa (right, dark-colored bars). B. Comparison of mining results for Angiosperms353 genes in simulated sequencing data at various depths with (right, dark-colored bars) and without (Depth only, left, light-colored bars) the application of the Weighted-node model. C. Comparative outcomes of mining Angiosperms353 genes at 50x coverage using simulated sequencing data with different degrees of variability, with (right, dark-colored bars) and without (left, light-colored bars) parameter-bootstrap verification. D. Heatmap depicting the quantity of high-quality data (level 1 ) obtained by GeneMiner using simulated sequencing data and reference sequences with different degrees of variability at diverse gradient depths.
Figure S1. The heatmaps for levels 2 through 4, indel rate, substitution rate, and recovered genes.