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. 2017 Sep 7;5:e3788. doi: 10.7717/peerj.3788

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©2017 Moller and Liang

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

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We evaluated seven different combinations of algorithms, implementations, and parameters. We evaluated both Crass and MinCED with default parameters. For MetaCRAST, we evaluated five different conditions differing in parallelization and metagenome loading method—BioPerl loading and 16 threads, BioPerl and a single thread, readfq with mce_open for loading and 16 threads, readfq with mce_open and a single thread, and readfq with the standard open routine and a single thread. The procedure for generating the simulated metagenomes is described in Materials and Methods. Run time was calculated as the sum of the user and system time (together the total CPU time). All data points represent the averages of three individual simulations and are presented with error bars representing two times the standard error above and two below the average.