I'm reading about cancer genomics and for better understanding of the subject decided to perform several numerical experiments. There are several naive questions that I would like to ask:
1) De novo assembly vs reads alignment - what is the preferred approach to assemble the whole tumor/normal genomes?
2) Is there any 'reads' simulator that allows to simulate cancer's genomes (with different types of aberrations, not only SNV) base on a reference one?
Thanks a lot, Maxim