What reference to be used in snippy

Question

[Optimist]

Hello all,

What logic must be used to select a genome as Reference genome in Snippy? Is it the NCBI ref genome or genome that has closest ANI value to the study genome that has to be used as reference. I want to use snippy to identify mutations in some particular set of genes and their effect on the CDS.

Thanking You all

Have a great Day!!!

Answer 1

[Kausik]

Hello,

Reference genome should be chosen according to the question we like to answer otherwise it is just another genome from which we want to find the difference. However there are certain basic features a reference genome must have.

1. It should be a complete genome
2. It should not be too many contigs and better, if it is a chromosome
3. The sequencing quality of the genome should be very good. If it is a hybrid genome of long and short reads then nothing like it.

If our question is to find out the effect ( genomic variation ) of a specific experimental condition on a strain and so on its genome ( eg. drug stress, some other chemical or physical stress) we must choose the closest genome of the strain and not a distant one. It is for the reason that more distant genome we take for this kind of questions, more extra variations will be detected. So we will end up having genomic variations arising out of evolution as well as the specific condition combined. But if we choose the closest ancestor of the genome/ strain/ species we cancel out the other effects and focus on only the conditions (eg. drug stress, some other chemical or physical stress).

If our question is broader then the reference genome would be different. The more closer genome we take, we get less variations. The more distant we go, we accumulate more variations. So will be true as we go from species to genus and further.

Kausik