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Something similar to the pf6+ notebooks, giving the data a narrative.

This might already be sufficiently covered by web app

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Produce PCoA plot and add in own samples

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Produce PCoA plot and add in own samples

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Tutorial on how to export data from Pf7 as a tabular file (for a gene or region of the genome) as many software tools expect tabular genotype files as input.

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Notebook for visualising FWS values

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something that we already do in Pf6+ (with phenotyper)

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Prevalence of drug resistance geographically

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Prevalence of drug resistance geographically

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Adding users own data into analysis
(This could be joint with some of the tasks under reproducing analysis)

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There is an example in the readme explaining why indels are important to include in analysis. There are specific locations used, could translate this example to a notebook

https://www.malariagen.net/sites/default/files/File8_Pf_6_README_20191010.txt

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Notebook showing how to regenerate genetic distance matrix with own parameters

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Convert current FWS code into a notebook that can be easily followed so people can reproduce FWS values

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how to open the npy genetic distance matrix, what is on there and what can you use that info

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There is a draft of this notebook, but needs reviewed