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. 2020 Mar 5;10:4165. doi: 10.1038/s41598-020-61159-z

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© The Author(s) 2020

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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The workflow shows the bioinformatics pipeline used to analyze the shotgun data generated from Illumina MiSeqDx. The pipeline consists of four components: (1) Sequence preprocessing, (2) Assembly and Annotation, (3) Alignment, and (4) Analysis and visualization.