Benchmarks of the 5-step pipeline on NA12878 exome (JP protocol).

In elPrep, the combined execution of all preparation steps is faster than running the steps one after the other. The execution of the five-step pipeline in elPrep does not take significantly longer than the execution of the two-step and three-step pipelines (Tables 2 and 3). elPrep executes the full pipeline between six times faster when using a similar amount of RAM as Picard (third column) and ten times faster when given access to all available RAM (fourth column). Benchmarks of the 5-step pipeline on NA12878 exome (JP protocol).