I noticed something that people need to be aware of when using chewBBACA for cgMLST-calling. When chewBBACA finds a new variant at a given locus, it gets the label "INF-NUMBER", where the number is the actual label of the variant. However, all samples run after the new variant that has the same variant, will only have the number label, without the "INF" in front. Be aware that when calculating distances from these data these two labels will be calculated as different, and not the same. Therefore they have to be changed before analysis.
I noticed something that people need to be aware of when using chewBBACA for cgMLST-calling. When chewBBACA finds a new variant at a given locus, it gets the label "INF-NUMBER", where the number is the actual label of the variant. However, all samples run after the new variant that has the same variant, will only have the number label, without the "INF" in front. Be aware that when calculating distances from these data these two labels will be calculated as different, and not the same. Therefore they have to be changed before analysis.