Benchmarks of the 3-step pipeline on NA12878 exome (Support protocol 3).

<p>In elPrep, the combined execution of all three preparation steps is faster than running the steps one after the other. Compared to Basic protocol 1 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132868#pone.0132868.t005" target="_blank">Table 1</a>), the extra step in this pipeline does not add an additional runtime cost when combining the execution of the steps with elPrep. elPrep executes the full pipeline five to seven times faster than using Picard, depending on how much RAM elPrep can use, namely the same amount as Picard (third column) or all available RAM (fourth column).</p><p>Benchmarks of the 3-step pipeline on NA12878 exome (Support protocol 3).</p

Benchmarks of the 2-step pipeline on NA12878 whole genome (Basic protocol 1).

<p>Similar as with exome data, the combined execution of the preparation pipeline in elPrep is much faster than executing the individual steps one by one, which is the only option with Picard. elPrep executes Basic protocol 1 about 2.5 times faster than Picard.</p><p>Benchmarks of the 2-step pipeline on NA12878 whole genome (Basic protocol 1).</p

Skeleton structure of a filter definition in elPrep.

<p>Skeleton structure of a filter definition in elPrep.</p

Benchmarks of the 3-step pipeline on NA12878 whole genome (Support protocol 3).

<p>The execution time with elPrep remains stable compared to Basic protocol 1 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132868#pone.0132868.t008" target="_blank">Table 4</a>). elPrep executes this preparation pipeline almost four times faster than Picard.</p><p>Benchmarks of the 3-step pipeline on NA12878 whole genome (Support protocol 3).</p

Benchmarks of the 2-step pipeline on NA12878 exome (Basic protocol 1).

<p>In elPrep, the combined execution of both preparation steps is faster than running the steps one after the other. When elPrep gets to use a similar amount of RAM as Picard uses, it executes the pipeline three times faster than Picard (third column). When elPrep is given access to all available RAM, it executes the pipeline five times faster than Picard (fourth column).</p><p>Benchmarks of the 2-step pipeline on NA12878 exome (Basic protocol 1).</p