My organism doesn't have a reference genome, but a closely related species, the deer mouse (approx. 4 my diverged), has one but only assembled at the scaffold level.
Is it better to align to a good quality ref. genome but that is about 50 my diverged (Ratus norv) assembled at the chromosome level, or to fraft genome of the less diverged one?
There are intermediates also, like the chinese hamster.
Thanks!
Is it better to align to a good quality ref. genome but that is about 50 my diverged (Ratus norv) assembled at the chromosome level, or to fraft genome of the less diverged one?
There are intermediates also, like the chinese hamster.
Thanks!
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