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FofanovLab / VaST

Variant Site Strain Typer: Identifies the minimum number of variable genomic site that are required to resolve a group of related bacterial strains
MIT License
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Use VaST on eukaryotes #6

Open nicola-debernardini opened 3 years ago

nicola-debernardini commented 3 years ago

Hi Tara,

I think your software is very interesting and perfectly fits the design of strain identification panels that I would like to generate for my set of Saccharomyces cerevisiae strains. However, I wonder weather you have any idea if the tool will work also on diploid organisms, such as eukaruotes, or if there is any trick to obtain a reliable results in this case.

I was wondering for example if the software could work properly if I provide a "variant_site_matrix.tsv" containing only the homozygous SNPs present in each strain.

Thank,

Nicola

tfursten commented 3 years ago

Hello Nicola, I am not very familiar with the biology or classification of yeast strains but I believe that you can still use the software with appropriate modifications. For example, if a given strain will always have a particular SNP (either homozygous or heterozygous), I would put that SNP in the variate site matrix. Then if you develop an assay to amplify that target, you would just need to account for the possibility of a heterozygous call for the SNP in your downstream analysis. Otherwise, if the genotype at a certain site varies and the strain may not always have the SNP, then I would do as you suggest and only use sites where the SNP is homozygous. Hope that helps, Tara