Using population genome graphs for genotyping

[ytliuSVN]

Dear curators,

I tried to dig deeper into the nature research paper (Bradley et al., 2015). In terms of mixed infection read analysis, the approach option(ii) aimed at directly compares the de Bruijn graph of the sample with the resistance informative reference graph. What does "compare" mean in genome graphs for genotyping?
Any suggestions would be appreciated.

[iqbal-lab]

Dear @ytliuSVN - where is this text

the approach option(ii) aimed at directly compares the de Bruijn graph of the sample with the resistance informative reference graph

from? I mean - where exactly? Mykrobe predictor compares susceptible/resistant alleles for SNPs/indels, and uses knowledge of local variation to inform the local graph. For genes, the idea is to detect what fraction of the gene is present, using all known "alleles" of the gene.

For "compare" with the resistance informative graph - I guess what you do is take the intersection, and then look at R or S alleles. Does that help?

[ytliuSVN]

Thanks for your detailed explanation.

This text appears in Figure 1 Representation and analysis of bacterial genetic variation. , especially emphasize on (b) In option (ii), we construct the de Bruijn graph of the sample and compare with the reference graph. Subsequently, we see a specific SNP is present both in the sample and the reference graph (marked X, Y).

Besides, when you detect what fraction of the gene is present that was associated with three competing models. Is that right?