Timing and memory usage to align two genome sequences for nucmer3 and nucmer4 compared to Mauve and Lastz aligners built using similar data structures.

We list both wall clock time and CPU time to show how effective is the code in utilizing multiple cores. Nucmer 4 is the fastest, but not the most memory efficient aligner. Nucmer3 failed to align human to chimp assembly due to the restriction on the size of the reference sequence. LASTZ and Mauve runs on human to chimp alignments took over two days, and we stopped them after that. LASTZ defaults are optimized for high sensitivity, resulting in slow performance. Thus for fairness of timing comparisons we ran LASTZ twice: once with default settings and once with parameters that result in sensitivity matching that of nucmer4 with default settings. We list the parameters in the supplement.