## 4 Experiments
\begin{table}
\begin{tabular}{c|c c c c c c} \hline \hline  & \multicolumn{5}{c}{**Problem**} \\ \hline
**Fragments** & 22,448 & 89,718 & 298,194 & 730,201 & 2,278,504 \\
**Contigs Obtained** & 82 & 114 & 163 & 224 & 512 \\
**Total Number of Bases** & 18,579 & 84,571 & 240,265 & 551,701 & 1,343,637 \\ \hline  & **Contigs Found** & 75 & 103 & 142 & 181 & 417 \\  & **\%** & 91.5 & 90.4 & 87.1 & 80.8 & 81.4 \\  & **Bases Found** & 15,599 & 72,245 & 174,244 & 320,502 & 791,376 \\
**Contigs** & **\%** & 84 & 85.4 & 72.5 & 58.1 & 58.9 \\
**Found** & **N50** & 356 & 1527 & 2984 & 3910 & 4135 \\  & **Average Length** & 208 & 701.4 & 1227.10 & 1770.70 & 1897.80 \\  & **Minimum Length** & 54 & 58 & 54 & 59 & 53 \\  & **Maximum Length** & 882 & 7,261 & 10,943 & 10,648 & 16,135 \\ \hline  & **Contigs not Found** & 7 & 11 & 21 & 43 & 95 \\  & **\%** & 8.5 & 9.6 & 12.9 & 19.2 & 18.6 \\  & **Bases not Found** & 2980 & 12,326 & 66,021 & 231,199 & 552,261 \\
**Contigs** & **\%** & 16 & 14.6 & 27.5 & 41.9 & 41.1 \\
**not Found** & **N50** & 539 & 2308 & 6336 & 8135 & 7554 \\  & **Average Length** & 425.7 & 1120.50 & 3143.90 & 5376.70 & 5813.30 \\  & **Minimum Length** & 95 & 96 & 103 & 181 & 251 \\  & **Maximum Length** & 826 & 3703 & 10,648 & 22,745 & 24,396 \\ \hline \hline \end{tabular}
\end{table} 
Table 9: Algorithm 1, \(F_{2}\) objective function, no transitive overlaps. In Experiment 3, we obtained the Minimum Spanning Tree (MST) from all overlaps using our version of [PERSON]'s algorithm. We only show the results for _F1_ (Tables 5 and 10). In this case, we were able to find much more bases in the genome than in previous experiments, including Edena, but the size of our _contigs_ is small. There appears to be a tradeoff between the number of bases that can be found and _contig_ length. In other experiments, we used Algorithm 4 without transitive overlaps, obtaining similar results to those of Algorithm 1 for _F1_ (_F1_ was again better than _F2_). Analyzing the _contigs_ obtained by the algorithm, we found that if the _contig_ is split at the edge that joins the cycle with the path, we have a better chance of finding both _contigs_. Therefore, we modified Algorithm 4 making d(v) = 0 in Step 2.2.1.1 and repeated Experiment 4 without transitive overlaps. In this case, the objective function _F1_ was better than _F2_ without being dominant. These results are given in Tables 5 and 11. In an analysis of those _contigs_ that were not found in the genome, we considered the possibility of splitting them in two or more pieces hoping that all of them could be found. There are few cases in which _contigs_ should be divided; in problem 730,201, using the modified Algorithm 4 with _F1_, there were 513 _contigs_ from which 414 were found directly, 76 were split in two to be found, 14 in three, 10 in four or more pieces, and two produced pieces that were too small to be considered. With appropriate rules, it should be possible to find the correct split points in most of the cases, as other assemblers do. We also analyzed residual paths, after removing paths of maximum length, from which we considered the possibility of recovering several long _contigs_, which we will do in the future.