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Computing time of de novo genome assemblies.

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posted on 08.09.2014, 03:10 by Sebastian Jünemann, Karola Prior, Andreas Albersmeier, Stefan Albaum, Jörn Kalinowski, Alexander Goesmann, Jens Stoye, Dag Harmsen

Based on the elapsed wall clock time (A, in hours) and the total CPU utilization (B, in percent and relative to the 48 available CPU cores of the executing compute host). With regard to the CPU utilization, all assemblies have been instructed via proper parameterization to make maximal use of the 48 available CPU cores. The only exceptions to this were SEQMAN, which does not support parallelization, and CELERA, which due to configuration constraints has altering concurrency and multi-threading parameters for different internal processes. For DBG assemblers only run time and CPU utilization of the single assemblies with the best performing k-mer parameter are shown and not the summation of the full k-mer optimization procedure (for SPADES and CLC this is equivalent).