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. 2021 Feb 16;13(3):evab028. doi: 10.1093/gbe/evab028

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© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 1. — The five step sangeranalyseR analysis workflow. (Column 1) The steps of a simple analysis using sangeranalyseR. The third step, exploring data through Shiny applications, is optional. (Column 2) The corresponding functions invoked in each step of the analysis in column 1. After preparing input files, users can run SangerRead, SangerContig, or SangerAlignment to start an analysis. The different functions produce objects containing a single read, a single contig, or a collection of aligned (and so assumed alignable contigs). Shiny applications are only available for the SangerContig and SangerAlignment objects. (Column 3) The input and/or output files that correspond to each step of the analysis.