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. 2019 Nov 8;9:16350. doi: 10.1038/s41598-019-52424-x

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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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SNPs trees of Salmonella reference datasets and data obtained with MinION. (a) Constructed with SNPs of twenty-three Salmonella reference datasets which were used for phylogenetic pipeline validation for foodborne pathogen surveillance³⁵; (b) The CFSAN000189 data is replaced with SNPs from the 240 mins and 1500 mins MinION-only assemblies obtained in this study; (c) The tree includes both the reference dataset and the MinION-only data for the CFSAN000189 strain along with the SNPs of the remaining 22 Salmonella reference datasets.