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. 2019 Mar 13;9:4318. doi: 10.1038/s41598-019-40739-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Effect of parameters on memory usage, performance and accuracy. (a) Peak memory usage of the index for different combinations of k and w. (b) Peak memory usage of the index for a large range of w with k = 15. (c) The effect of w on sensitivity and error relative to the default window size. The x-axis is the minimiser window size (w). The k-mer size is held constant at 15 for all values of w. The y-axis shows the number of missing mappings/mismatches or extra mapping (compared to the mappings from default w = 10) as a percentage of the number of reads. (d) Distribution of the dynamic programming alignment score for different minimiser window sizes (w). The x-axis is the score and the y-axis is the smoothed number of mappings for a particular score. Note that the distribution is smoothed to show the trend. (e) Effect of the number of threads on memory and performance. The parameters k, w and K were held constant at 15, 25 and 200 M respectively while changing the number of threads. Both the peak memory usage and the runtime were measured on a PC with an Intel i7-6700 CPU and 16 GB of RAM. (f) Effect of the number of query bases loaded at a time. The parameters k, w and t were held constant at 15, 25 and 8 respectively.