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What a nice readme! well done. Your scripts documentation is also very well done and helpful. Very well! However, unfortunately, it seems you didn't include a figure made in R with your data, and neither a .md summary discussion of your analyses and preliminary results. This is a shame since the rest of your final work was nice.
Other things you could improve:
- Your meta information in id_samples.txt is very poor. You could add columns with the reference for published genomes, sampling locality, whether it is wild or landrace, etc.
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