# Reference Mapping Considering Swaps of Adjacent Bases
## 3 Results  
The data used in these experiments were the human genome sequence and the drosophila genome sequence. The human genome sequence is GRCh38 (3.3 GB), and 100 bp-paired-end reads (SRR211279, 8.7 GB each) containing 25,467,888 reads in total. The reads were generated by Illumina GAIK from the Washington University Genome Sequencing Center. The drosophila genome sequence is DhydRS2 (148.5 MB, Drosophila hydei), and 100 bp-paired-end reads (SRR6326389, 12.7 GB each) containing 38,873,031 reads in total. The reads were generated by Illumina HiSeq 2500 from Texas A&M University. In order to examine the performance and effectiveness of SOAP3-swap, the algorithm was compared to SOAP3-dp, SOAP3, CUSHAW2-GPU, BarraCUDA, BWA, Bowtie2, and CUSHAW2. The experimental conditions were as follows:  
* CPU and RAM: AMD Ryzen 9 3950X (3.5 GHz), 64 GB RAM (2666 MHz);
* OS: Fedora 27 (64 bit);
* GPU: GeForce RTX 2080 Ti (11 GB memory);
* Development tools and language: C++ (GCC 7.4.0), CUDA (SDK 9.1). SOAP3-swap, SOAP3-dp, CUSHAW2-GPU, and BarraCUDA were tested using 32 CPU threads and one GPU device. SOAP3 was tested using six CPU threads, which were maximal and one GPU device. BWA, Bowtie2, and CUSHAW2 were tested using 32 CPU threads. In SOAP3-swap and SOAP3-dp, \(S_{MA}\) was set to 1, and \(S_{MI}\), \(S_{GO}\), and \(S_{GE}\) were set to \(-2\), \(-3\), and \(-1\), respectively, as in [16]. In SOAP3-swap, \(S_{SW}\) was tested at \(-1\), \(-2\), and \(-3\). Users can adjust the penalty scores to determine which operation is more likely to occur. The average running time of 20 experiments was taken to represent the running time of each tool. Tables 1 and 2 show the running times and alignment ratios of the paired-end alignments produced by the various tools for the human genome and for the drosophila genome, respectively. Table 3 shows the number of read pairs including at least one swap according to the swap cost and the swapped block size for the human genome and the drosophila genome. \begin{table}
\begin{tabular}{c c c c c} \hline \hline  & \multicolumn{3}{c}{**Paired-End Reads**} & \\ \cline{2-4}
**Tools** & **Runtime (s)** & **Number of Aligned Reads (Ratio)** & **Difference from SOAP3-dp** & **GPU-Based** \\ \hline SOAP3-swap & \multirow{2}{*}{186.98} & 25,105,846 & \multirow{2}{*}{\(+\)4667} & \multirow{2}{*}{Yes} \\ (Full SA, \(S_{SW}=-1\)) & & (98.58\%) & & \\ \hline SOAP3-swap & \multirow{2}{*}{178.79} & 25,103,497 & \multirow{2}{*}{\(+\)2318} & \multirow{2}{*}{Yes} \\ (Full SA, \(S_{SW}=-2\)) & & (98.57\%) & & \\ \hline SOAP3-swap & \multirow{2}{*}{181.08} & 25,102,151 & \multirow{2}{*}{\(+\)972} & \multirow{2}{*}{Yes} \\ (Full SA, \(S_{SW}=-3\)) & & (98.56\%) & & \\ \hline SOAP3-dp & \multirow{2}{*}{178.52} & 25,101,179 & \multirow{2}{*}{\(\cdot\)} & \multirow{2}{*}{Yes} \\ (Full SA) & & (98.56\%) & & \\ \hline SOAP3 & \multirow{2}{*}{212.22} & 22,613,051 & \multirow{2}{*}{\(-\)2,488,128} & \multirow{2}{*}{Yes} \\ (Full SAW2-GPU & \multirow{2}{*}{599.94} & 24,957,932 & \multirow{2}{*}{\(-\)143,247} & \multirow{2}{*}{Yes} \\ (98.00\%) & & & \\ \hline BarraCUDA & \multirow{2}{*}{947.67} & 24,551,512 & \multirow{2}{*}{\(-\)549,667} & \multirow{2}{*}{Yes} \\ (96.40\%) & & & \\ \hline BWA & \multirow{2}{*}{2731.73} & 24,598,492 & \multirow{2}{*}{\(-\)502,687} & \multirow{2}{*}{No} \\ (96.59\%) & & & \\ \hline Bowtie2 & \multirow{2}{*}{1414.67} & 24,798,944 & \multirow{2}{*}{\(-\)302,235} & \multirow{2}{*}{No} \\ (Sensitive) & & (97.37\%) & & \\ \hline CUSHAW2 & \multirow{2}{*}{2084.69} & 24,133,013 & \multirow{2}{*}{\(-\)968,166} & \multirow{2}{*}{No} \\ (94.76\%) & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Comparison of SOAP3-swap and other tools for the human genome.