Hi, I would like to generate a set of metrics to be able to evaluate the general quality of a whole genome sequence before I can start analyzing it with a reasonable confidence that the variation I am after is in the haystack. I know there are tools like fastqc that generate reports but without knowing pretty well what you should expect the tools are less effective. I know there is not a single criteria and everyone has their own list of things but I think there are some common criteria that most people could aggree on.
example GC% should be between 40-50 or total number of reads should be >3 million etc. Thanks