Merge branch 'main' of https://github.com/ISUgenomics/Zengyi-2021-Sch…

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Notebook_Maryam/methods.md

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 ## Comparing genomes using dotplot
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 We used [re-DOT-able](https://www.bioinformatics.babraham.ac.uk/projects/redotable/) to compare the reference genome and assembled genome for each strain.
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 In order to visualize pairwise comparison between sequences we used a desktop app ([re-DOT-able](https://www.bioinformatics.babraham.ac.uk/projects/redotable/) ) from Babraham Bioinformatics to plot  interactively and also save the plots as images. We made pairwise comparisons between the reference genome and each of the seven assembled genomes to look for insert location and for any genome re-arrangements. In order to check the location Additionally we also plotted each assembly against the relevant insert sequences. For detailed information; Simon Andrews, the developer has a really good [video tutorial](https://www.youtube.com/watch?v=qPxl2hflG9Q&feature=emb_logo).
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