If I have:
- Pooled DNA from multiple different but genetically related (sibling) individuals, sequenced in one sequencing run
- DNA from another individual (genetically related (sibling) to those in the pool), sequenced on its own
Then If I assemble the single individual and map the pooled data to it, would I see greater (depth and breadth) of coverage across the genome assembly for the pool (assuming normalisation between read libraries) than if I were to sequence just one of those individuals from the pool and map that data to the assembly? (i.e. the pooled reads are more likely to cover the regions of the genome covered by the assembly because there's a pool of individuals)
Is there a biological reason for obtaining a slightly different representation of the genome for each of those individuals in the pool - for example, that would confound DNA extraction in a specific way for each individual such that coverage is affected?