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B-UMMI / chewBBACA_tutorial

Step by step tutorial using chewBBACA with all necessary files and results
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Mistake in the tutorial at Evaluate genome quality / missing step? #9

Open dutchscientist opened 3 years ago

dutchscientist commented 3 years ago

Hi,

Am doing the tutorial with my own dataset (Staphylococci) and it is great. However, at the "Evaluate genome quality" step I struggled with two things:

1) it is unclear how the removedGenomes_25.txt is created; I created it manually, but there is no clear instruction on how to generate it. A comment may be helpful. 2) the command line "chewBBACA.py ExtractCgMLST -i cgMLST_all.tsv -o cgMLST_25 -g removedGenomes_25.txt" is incorrect, the "-g" should be "--g" (double hyphen)

Just the icing on the cake! :)

ramirma commented 3 years ago

Thank you for the heads-up @dutchscientist. We were planning to go over the documentation soon to update and revise it and we will certainly look correct the two issues you point out. I will leave the issue open until we do.