I am reading the Whole Genome Sequencing for de novo Assembly Best Practices
- Use the Sequel II or IIe System and SMRT® Cell 8M to sequence to desired coverage depth for complexity of genome
- 10- to 15-fold coverage per haplotype recommended
First of all Wikipedia shows different definitions for the term haplotype. Which one applies here?
Second while the recommendations state to use
10- to 15-fold coverage per haplotype I find myself confused about how I would know the haplotype beforehand.
From what I understand of haplotype-estimation I would need the sequenced data first.
How would I go about this when wanting to do a de novo assembly of a species that has no published assembly of any close relatives? That means the only information I would have at that point is the C-value of the species to be sequenced.
Or better, how does the Sequel II figure out the number of haplotypes for achieving the desired fold-coverage?
I hope I'm in the right SE.