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.