# Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance
## 4 Discussion
### Comparing Alignment Accuracy  
Regarding the results from Section 3.2, Minimap2's ksw mapping accuracy was satisfactory on the simulated dataset with an overall correct mapping position for 99.05% of the reads, considering that it is correctly mapped when there is an overlap of above 90% of the original region. It was not possible to evaluate this performance on the real datasets due to the lack of truth. \begin{table}
\begin{tabular}{l l l l l l l l l l l} \hline \hline  & \multicolumn{2}{c}{**Number of Threads (sw)**} & \multicolumn{1}{c}{**1**} & \multicolumn{1}{c}{**2**} & \multicolumn{1}{c}{**3**} & \multicolumn{1}{c}{**4**} & \multicolumn{1}{c}{**5**} & \multicolumn{1}{c}{**6**} & \multicolumn{1}{c}{**7**} & \multicolumn{1}{c}{**8**} \\ \hline \multirow{7}{*}{Simulated PacBio} & software & total execution (s) & 759.157 & 390.198 & 266.926 & 206.255 & 197.863 & 186.727 & 177.508 & 169.927 \\ \cline{2-11}  & \multirow{2}{*}{1 kernel} & total execution (s) & 539.56 & 299.76 & 233.88 & 208.93 & 203.74 & 253.84 & 409.03 & 453.26 \\  & & acceleration & 1.41 & 1.30 & 1.14 & 0.99 & 0.97 & 0.74 & 0.43 & 0.37 \\  & & thread acceleration & 1.00 & 1.80 & 2.31 & 2.58 & 2.65 & 2.13 & 1.32 & 1.19 \\ \cline{2-11}  & \multirow{2}{*}{2 kernels} & total execution (s) & 538.996 & 289.557 & 211.837 & 198.700 & 203.366 & 228.516 & 273.066 & 313.150 \\  & & acceleration & 1.41 & 1.35 & 1.26 & 1.04 & 0.97 & 0.82 & 0.65 & 0.54 \\  & & thread acceleration & 1.00 & 1.86 & 2.54 & 2.71 & 2.65 & 2.36 & 1.97 & 1.72 \\ \hline \multirow{7}{*}{Real ONT} & software & total execution (s) & 3105.50 & 1559.59 & 1056.77 & 806.37 & 774.30 & 719.29 & 684.98 & 646.35 \\ \cline{2-11}  & \multirow{2}{*}{1 kernel} & total execution (s) & 2243.69 & 1,168.48 & 837.14 & 712.91 & 653.68 & 660.44 & 937.68 & 1258.13 \\  & & acceleration & 1.38 & 1.33 & 1.26 & 1.13 & 1.18 & 1.09 & 0.73 & 0.51 \\  & & thread acceleration & 1.00 & 1.92 & 2.68 & 3.15 & 3.43 & 3.40 & 2.39 & 1.78 \\ \cline{2-11}  & \multirow{2}{*}{2 kernels} & total execution (s) & 2197.265 & 1126.070 & 794.728 & 638.109 & 586.025 & 576.393 & 672.990 & 858.846 \\  & & acceleration & 1.41 & 1.38 & 1.33 & 1.26 & 1.32 & 1.25 & 1.02 & 0.75 \\  & & thread acceleration & 1.00 & 1.95 & 2.76 & 3.44 & 3.75 & 3.81 & 3.26 & 2.56 \\ \hline \multirow{7}{*}{Real PacBio} & software & total execution (s) & 4255.21 & 2132.71 & 1431.38 & 1083.29 & 1037.82 & 965.57 & 904.33 & 858.31 \\ \cline{2-11}  & \multirow{2}{*}{1 kernel} & total execution (s) & 3570.25 & 1,813.39 & 1243.76 & 1003.40 & 919.39 & 889.68 & 1077.63 & 1575.97 \\ \cline{1-1}  & & acceleration & 1.19 & 1.18 & 1.15 & 1.08 & 1.13 & 1.09 & 0.84 & 0.54 \\ \cline{1-1}  & \multirow{2}{*}{2 kernels} & total acceleration & 1.00 & 1.97 & 2.87 & 3.56 & 3.88 & 4.01 & 3.31 & 2.27 \\ \cline{1-1} \cline{2-11}  & \multirow{2}{*}{2 kernels} & total execution (s) & 3470.799 & 1765.341 & 1239.144 & 994.346 & 885.107 & 831.761 & 855.454 & 1117.282 \\ \cline{1-1}  & & acceleration & 1.23 & 1.21 & 1.16 & 1.09 & 1.17 & 1.16 & 1.06 & 0.77 \\ \cline{1-1}  & & thread acceleration & 1.00 & 1.97 & 2.80 & 3.49 & 3.92 & 4.17 & 4.06 & 3.11 \\ \hline \hline \end{tabular}
\end{table} 
Table 6: Execution times and acceleration in the Minimap2-GACT-X integrated system. GACT-X's alignment scores were very similar to Minimap2's ksw on the simulated data, considerably worse on the real ONT data, and dissimilar but equivalent on the real PacBio data since there was a high rate of alignments that were worse and better. The absence of a second affine gap function in GACT-X might be responsible for most of the performances with worse alignment scores since the comparison was performed considering this second gap function. GACT-X's tile and banding heuristics can also perform differently in comparison to Minimap2's chaining and banding techniques, but a fairer comparison could be done with equal alignment parameters in the future. Regarding query alignment lengths, both algorithms presented similar distributions on the two PacBio datasets.