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Make materials consistent throughout #62

@tavareshugo

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@tavareshugo

At the moment the "Clinical Isolates" sections are not quite matching the "Case Studies" in terms of where the output files are stored and also how the data is organised on Dropbox. It might be good to make these consistent with each other, in case we run this workshop again.

The exercises could also be revised to use "small" versions of the datasets, and two versions either for Illumina or ONT.
Some preprocessed files with larger sample sizes could be included for the phylogeny section, for example.

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