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.