Time and memory consumption of gap closure software. Comparative analysis of the runtime and memory usage per dataset based on a single iteration. SOAPdenovo needs a shorter time to complete the analysis if the amount of data is very small or large, whereas GapFiller is faster for intermediate data sizes (10 to 20 million reads). With regard to memory usage, GapFiller outperforms SOAPdenovo since intermediate output is temporarily stored (and not kept in the memory). For all datasets analyzed, GapFiller requires only 0.1 GB of memory, which is mostly consumed by the Burrows-Wheeler Aligner (BWA). Note that no results are displayed for IMAGE since the method can not handle multiple libraries and requires very large computation times to complete the process. M, million.
Boetzer and Pirovano Genome Biology 2012 13:R56 doi:10.1186/gb-2012-13-6-r56