Results
Performance comparison of different tools
In Test I, we evaluated the operational performance and computational results of GeneMiner with those of aTRAM, Easy353, and HybPiper (Table 1). Figure 1-B displays the average values for the speed, memory usage, and disk space usage required for each tool when analyzing two species:A. thaliana and O. sativa. GeneMiner exhibited the fastest speed, being on average 1.8, 4.52, and 42.62 times faster than Easy353, HybPiper, and aTRAM, respectively. GeneMiner also exhibited disk usage under 1 GB and higher memory usage than both HybPiper and aTRAM, ranging between (6.91-7.78 GB). For the assembly results (Figure 3-A), GeneMiner acquired the highest number of bases (382,013 and 417,976), provided the highest accuracy (average 99.17%) and sequence coverage (average 99.92%), and the lowest indel rate (average 0.64%) and substitution rate (average 0.20%). In terms of the number of genes acquired, for both species, aside from aTRAM which performed poorly on A. thaliana , securing only 303 genes, all other methods managed to capture more than 90% of the genes. Among them, GeneMiner had the highest recovery rate, recovering 349 and 346 genes from A. thaliana andO. sativa , respectively. The number of high-quality sequences, rated as level 1 (303 and 313), was significantly higher than the other software packages, and the number of low-quality sequences, rated as level 4 (20 and 18), was significantly lower compared to the other tools.