How can I analyse whole genome sequences using R?
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You should also explain what kind of data you have. Depending on that information the answers you need can go in all directions. Do you have raw reads, assembled genomes? Is there a reference available or you are going to do an all to all comparison? What is the mail goal of this exercise?
Thank you, I have assembled genomes and I have the reference available. I want to compare my test samples against the reference. The main goal is to determine if there is any variation or similarity between the samples and the reference. and if there is variability what are these genes?
You could do it with R, but it’s probably easier to use commandline tools.
Do you have some idea of how variable this clade is likely to be? Are we talking SNP differences or major recombination?