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. 2019 May 24;9:7808. doi: 10.1038/s41598-019-44189-0

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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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Illustration of the k-mer frequency method used to select conserved sequences in the reference genome for an example using 3-mers, a hypothetical set of 4 short genome assemblies and a frequency cutoff of 95% (in practice, canonical but longer k-mers are used to favor unique mappings to the genome). The function ‘k-mer frequency’ represents the relative frequency of the reference genome k-mers in the genome assembly set, and the function ‘conservation score’ is generated from this by taking a running maximum in an interval of 3 nucleotides.