What will happen when using chewBBACA with a diploid genome?

[dutchscientist]

I am playing with chewBBACA and Candidozyma/Candida genomes, of which some species like C. auris are always haploid, while others like C. albicans can be diploid. For C. auris, I am making progress towards a cgMLST scheme, but I wonder what would happen with diploid genomes. Can chewBBACA return two different alleles, is there a setting for that?

Just a hobby project for now, but I can see people working on eukaryotic pathogens (parasites/nematodes etc) being interested :)

[ramirma]

@dutchscientist chewBBACA was not designed to work with diploid organisms, so there is no specific way in which it will the encode the presence of two different alleles in the same organism. There are of course other problems in working with eukaryotes that need to be addressed. It is something that we have given some thought to on and off over the years.

[dutchscientist]

@ramirma thanks, that's what I thought, unsuited for diploid organisms. No problem, always good to be aware of the limitations! That is why I am trying C. auris, as that is primary haploid. I have worked with chewBBACA using a minimal ORF size of 450 nt and translation table 12, and that seems to work nicely when I design a scheme, got ~4200 markers that I now will compare with the annotated features. A quick run does reproduce the clades I-VI described in the literature.